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Aug 14, 2019 09:08 AM | Tinya Chang
Problem with preprocessing
Dear experts,
I keep getting the following error messages:
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
How do I get pass them? I have no problems with preprocessing data in the tutorial pack, but when I try to preprocess my own data set, it just does not work.
Thanks in advance!
Kind regards,
Tinya
I keep getting the following error messages:
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
How do I get pass them? I have no problems with preprocessing data in the tutorial pack, but when I try to preprocess my own data set, it just does not work.
Thanks in advance!
Kind regards,
Tinya
Aug 16, 2019 09:08 AM | Anton Albajes-Eizagirre - FIDMAG - Germanes Hospitalaries
RE: Problem with preprocessing
Hello Tinya,,
What operation are you performing when you get these errors? They appear to be errros from the threshold operation rather thant from the preprocessing operation.
Can you paste the log?
Best,
Anton
Originally posted by Tinya Chang:
What operation are you performing when you get these errors? They appear to be errros from the threshold operation rather thant from the preprocessing operation.
Can you paste the log?
Best,
Anton
Originally posted by Tinya Chang:
Dear experts,
I keep getting the following error messages:
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
How do I get pass them? I have no problems with preprocessing data in the tutorial pack, but when I try to preprocess my own data set, it just does not work.
Thanks in advance!
Kind regards,
Tinya
I keep getting the following error messages:
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
How do I get pass them? I have no problems with preprocessing data in the tutorial pack, but when I try to preprocess my own data set, it just does not work.
Thanks in advance!
Kind regards,
Tinya
Sep 3, 2019 03:09 PM | Brandon Gunasekera
RE: Problem with preprocessing
Hi Anton,
Has a solution to this problem been identified? I have this when thresholding. Here is the execution log:
Best wishes,
Brandon
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [txt] = [foobin] * [E:/THC]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [E:/THC] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [txt] = [foobin] * [E:/THC]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [E:/THC] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir C:\Users\k1754869\sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
Prior open browser
After open browser
o
aCalling MRICron to display 3D results
Mricron call: "C:/Users/k1754869/Downloads/win/mricron/mricron.exe" C:\Users\k1754869\Downloads\SdmPsiGui-win64-v6.11\SdmPsiGui-win64-v6.11\bin\windows64\..\..\/share/sdm_template.nii.gz -o E:/THC txt folder/analysis_THC_Mean/THC_Mean_z_p_0.05000_10.nii.gz -o E:/THC txt folder/analysis_THC_Mean/THC_Mean_z_p_0.05000_10_neg
Has a solution to this problem been identified? I have this when thresholding. Here is the execution log:
Best wishes,
Brandon
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [txt] = [foobin] * [E:/THC]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [E:/THC] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [txt] = [foobin] * [E:/THC]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [E:/THC] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir C:\Users\k1754869\sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
Prior open browser
After open browser
o
aCalling MRICron to display 3D results
Mricron call: "C:/Users/k1754869/Downloads/win/mricron/mricron.exe" C:\Users\k1754869\Downloads\SdmPsiGui-win64-v6.11\SdmPsiGui-win64-v6.11\bin\windows64\..\..\/share/sdm_template.nii.gz -o E:/THC txt folder/analysis_THC_Mean/THC_Mean_z_p_0.05000_10.nii.gz -o E:/THC txt folder/analysis_THC_Mean/THC_Mean_z_p_0.05000_10_neg
Sep 13, 2019 03:09 AM | Rebecca Hu
RE: Problem with preprocessing
Hi Anton,
I am having the same issue with the threshold step with the newest version of SDM-PSI. Has any solution been found? Thank you!
Best,
Rebecca
I am having the same issue with the threshold step with the newest version of SDM-PSI. Has any solution been found? Thank you!
Best,
Rebecca
Sep 13, 2019 04:09 AM | Rebecca Hu
RE: Problem with preprocessing
The execution log:
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [meta-analysis/Data/Rebecca_FA_BD_HV/analysis_BD_FA_mean/BD_FA_mean_z] = [foobin] * [/Users/rebecca/Documents/MRSP/DTI]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [/Users/rebecca/Documents/MRSP/DTI] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [meta-analysis/Data/Rebecca_FA_BD_HV/analysis_BD_FA_mean/BD_FA_mean_z] = [foobin] * [/Users/rebecca/Documents/MRSP/DTI]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [/Users/rebecca/Documents/MRSP/DTI] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir /Users/rebecca/.libsdm/sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
o
aCalling MRICron to display 3D results
c
wmricron program not found
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [meta-analysis/Data/Rebecca_FA_BD_HV/analysis_BD_FA_mean/BD_FA_mean_z] = [foobin] * [/Users/rebecca/Documents/MRSP/DTI]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [/Users/rebecca/Documents/MRSP/DTI] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [meta-analysis/Data/Rebecca_FA_BD_HV/analysis_BD_FA_mean/BD_FA_mean_z] = [foobin] * [/Users/rebecca/Documents/MRSP/DTI]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [/Users/rebecca/Documents/MRSP/DTI] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir /Users/rebecca/.libsdm/sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
o
aCalling MRICron to display 3D results
c
wmricron program not found
Nov 4, 2019 07:11 AM | e0046902
RE: Problem with preprocessing
Originally posted by Rebecca Hu:
Is there a solution to this problem yet? I have been experiencing the same errors.
Thanks for any advice.
The execution log:
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [meta-analysis/Data/Rebecca_FA_BD_HV/analysis_BD_FA_mean/BD_FA_mean_z] = [foobin] * [/Users/rebecca/Documents/MRSP/DTI]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [/Users/rebecca/Documents/MRSP/DTI] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [meta-analysis/Data/Rebecca_FA_BD_HV/analysis_BD_FA_mean/BD_FA_mean_z] = [foobin] * [/Users/rebecca/Documents/MRSP/DTI]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [/Users/rebecca/Documents/MRSP/DTI] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir /Users/rebecca/.libsdm/sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
o
aCalling MRICron to display 3D results
c
wmricron program not found
Hi users,IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [meta-analysis/Data/Rebecca_FA_BD_HV/analysis_BD_FA_mean/BD_FA_mean_z] = [foobin] * [/Users/rebecca/Documents/MRSP/DTI]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [/Users/rebecca/Documents/MRSP/DTI] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [meta-analysis/Data/Rebecca_FA_BD_HV/analysis_BD_FA_mean/BD_FA_mean_z] = [foobin] * [/Users/rebecca/Documents/MRSP/DTI]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [/Users/rebecca/Documents/MRSP/DTI] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir /Users/rebecca/.libsdm/sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
o
aCalling MRICron to display 3D results
c
wmricron program not found
Is there a solution to this problem yet? I have been experiencing the same errors.
Thanks for any advice.
Nov 19, 2019 02:11 PM | Arnaud Leroy
RE: Problem with preprocessing
Hi,
I am experiencing the same issue with the same log (I'm using linux). Is there any way to fix this issue?
I am experiencing the same issue with the same log (I'm using linux). Is there any way to fix this issue?
Nov 26, 2019 08:11 AM | Anton Albajes-Eizagirre - FIDMAG - Germanes Hospitalaries
RE: Problem with preprocessing
Hello,
Could you tell us what is the name of the model you are trying to threshold? If you could send to antonae@gmail.com the complete listing (with subfolders) of the data folder, and the contents of the sdmpsi_params.xml file we could give it a look.
Thanks,
Anton
Could you tell us what is the name of the model you are trying to threshold? If you could send to antonae@gmail.com the complete listing (with subfolders) of the data folder, and the contents of the sdmpsi_params.xml file we could give it a look.
Thanks,
Anton
Dec 5, 2019 09:12 PM | Hongru Zhu
RE: Problem with preprocessing
Hi Anton,
I have the same problem. My Os is Windows 10 64. Are there any solutions?
Thanks
Hongru
Home dir C:\Users\zhuho\sdm.conf
Loading study mask gray_matter_2mm
Executing Perm for MyTest with vars ,,, and hyp[1.000000,0.000000,0.000000,0.000000,0.000000]
9 studies included
Using 8 threads
aRecreating studies
file D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/indexes_gray_matter_2mm.bin
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oRecreating studies
aLoading imputations
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oLoading imputations
aGetting Null distributions with 8 threads
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oGetting Null distributions
Path to save analysis_MyTest/fwe/maxsMinsZ.asc
aPerforming P-correction
oPerforming P-correction
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
Done!
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_MyTest/MyTest_z] = [foobin] * [D:/Google]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [D:/Google] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_MyTest/MyTest_z] = [foobin] * [D:/Google]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [D:/Google] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir C:\Users\zhuho\sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
Prior open browser
After open browser
o
aCalling MRICron to display 3D results
Mricron call: "C:/Users/zhuho/Documents/win/mricron/mricron.exe" D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/sdm_template.nii.gz -o D:/Google Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_MyTest/MyTest_z_p_0.05000_10.nii.gz -o D:/Google Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_MyTest/MyTest_z_p_0.05000_10_neg.nii.gz
o
d
getprogdir entry argv D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64/sdm_core
getprogdir exit pdir D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1
Home dir C:\Users\zhuho\sdm.conf
aConducting globals analysis
o
aCalling web browser to display the report
Prior open browser
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d
Home dir C:\Users\zhuho\sdm.conf
Home dir C:\Users\zhuho\sdm.conf
Home dir C:\Users\zhuho\sdm.conf
Load atlas D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/atlas_aal_cts_2mm.nii.gz
length 902629 sdm1_lengt 902629
aAnalyzing coordinates
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aCreating anisotropic space
sdm_s_dir got D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\
Path for cor template D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/cor_gray_matter_2mm.nii.gz
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aPreprocessing studies
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%27% Estimated remaining time(s): 91 (ETA 2019-12-05 11:41:49)
%36% Estimated remaining time(s): 64 (ETA 2019-12-05 11:41:24)
%45% Estimated remaining time(s): 46 (ETA 2019-12-05 11:41:08)
%54% Estimated remaining time(s): 35 (ETA 2019-12-05 11:41:01)
%63% Estimated remaining time(s): 29 (ETA 2019-12-05 11:41:03)
%72% Estimated remaining time(s): 31 (ETA 2019-12-05 11:41:36)
%81% Estimated remaining time(s): 19 (ETA 2019-12-05 11:41:27)
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
o
aCalling web browser to display the report
Prior open browser
After open browser
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d
getprogdir entry argv D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64/sdm_core
getprogdir exit pdir D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1
Home dir C:\Users\zhuho\sdm.conf
aConducting globals analysis
o
aCalling web browser to display the report
Prior open browser
After open browser
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d
Home dir C:\Users\zhuho\sdm.conf
Home dir C:\Users\zhuho\sdm.conf
Home dir C:\Users\zhuho\sdm.conf
Load atlas D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/atlas_aal_cts_2mm.nii.gz
length 902629 sdm1_lengt 902629
aAnalyzing coordinates
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aCreating anisotropic space
sdm_s_dir got D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\
Path for cor template D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/cor_gray_matter_2mm.nii.gz
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aPreprocessing studies
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%18% Estimated remaining time(s): 31 (ETA 2019-12-05 11:52:16)
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Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
o
aCalling web browser to display the report
Prior open browser
After open browser
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d
Home dir C:\Users\zhuho\sdm.conf
iExecuting mle for 'OCDTest' with var1 '' var2 '' var3 '' var4 '' hyp=[1.000000,0.000000,0.000000,0.000000,0.000000] and filter ''
Loading study mask gray_matter_2mm
aStarting MLE...
Using 8 threads
ncoef: 1
aEstimating coefficients...
nLoo: 1
%9% Estimated remaining time(s): 20 (ETA 2019-12-05 11:54:03)
%18% Estimated remaining time(s): 18 (ETA 2019-12-05 11:54:03)
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%36% Estimated remaining time(s): 10 (ETA 2019-12-05 11:53:57)
%45% Estimated remaining time(s): 9 (ETA 2019-12-05 11:53:58)
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%81% Estimated remaining time(s): 3 (ETA 2019-12-05 11:53:58)
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oEstimating coefficients...
aEstimating tau2...
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%100% Estimated remaining time(s): 0 (ETA 2019-12-05 11:54:21)
%101% Estimated remaining time(s): -1 (ETA 2019-12-05 11:54:21)
oEstimating tau2...
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
incl is 10
dMLE
Loading study mask gray_matter_2mm
iExecuting MI for s_name OCDTest with 50 imputs and filter ''
aStarting MI... with nImputs 50
10 studies included in MI
%1% Estimated remaining time(s): 0 (ETA 2019-12-05 11:54:24)
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%17% Estimated remaining time(s): 581 (ETA 2019-12-05 12:06:04)
%18% Estimated remaining time(s): 660 (ETA 2019-12-05 12:07:49)
%19% Estimated remaining time(s): 690 (ETA 2019-12-05 12:08:36)
%20% Estimated remaining time(s): 656 (ETA 2019-12-05 12:08:04)
%21% Estimated remaining time(s): 616 (ETA 2019-12-05 12:07:24)
%22% Estimated remaining time(s): 581 (ETA 2019-12-05 12:06:49)
%23% Estimated remaining time(s): 549 (ETA 2019-12-05 12:06:17)
%24% Estimated remaining time(s): 519 (ETA 2019-12-05 12:05:47)
%25% Estimated remaining time(s): 492 (ETA 2019-12-05 12:05:20)
%26% Estimated remaining time(s): 489 (ETA 2019-12-05 12:05:25)
%27% Estimated remaining time(s): 548 (ETA 2019-12-05 12:06:55)
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%50% Estimated remaining time(s): 408 (ETA 2019-12-05 12:08:00)
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%85% Estimated remaining time(s): 115 (ETA 2019-12-05 12:07:14)
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%90% Estimated remaining time(s): 82 (ETA 2019-12-05 12:08:04)
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%99% Estimated remaining time(s): 8 (ETA 2019-12-05 12:08:10)
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
dMI
Loading study mask gray_matter_2mm
iRunning meta for OCDTest with var1 '' var2 '' var3 '' var4''
10 studies included in meta
aMeta
%2% Estimated remaining time(s): 0 (ETA 2019-12-05 12:08:04)
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%24% Estimated remaining time(s): 19 (ETA 2019-12-05 12:08:29)
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Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
dMeta
Loading study mask gray_matter_2mm
aPool
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a(imgcalc) [analysis_OCDTest/uncorrp.nii.gz] = "1-p values" from "z scores" in [analysis_OCDTest/OCDTest_z.nii.gz]
o
a(imgcalc) [analysis_OCDTest/uncorrp_neg.nii.gz] = 1 - [analysis_OCDTest/uncorrp.nii.gz]
o
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
dPool
Home dir C:\Users\zhuho\sdm.conf
Loading study mask gray_matter_2mm
Executing Perm for OCDTest with vars ,,, and hyp[1.000000,0.000000,0.000000,0.000000,0.000000]
10 studies included
Using 9 threads
aRecreating studies
file D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/indexes_gray_matter_2mm.bin
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%90% Estimated remaining time(s): 3 (ETA 2019-12-05 12:10:06)
oRecreating studies
aLoading imputations
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oLoading imputations
aGetting Null distributions with 9 threads
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%63% Estimated remaining time(s): 1958 (ETA 2019-12-05 13:38:19)
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%88% Estimated remaining time(s): 630 (ETA 2019-12-05 13:37:39)
%89% Estimated remaining time(s): 577 (ETA 2019-12-05 13:37:37)
%90% Estimated remaining time(s): 525 (ETA 2019-12-05 13:37:38)
%91% Estimated remaining time(s): 472 (ETA 2019-12-05 13:37:36)
%92% Estimated remaining time(s): 419 (ETA 2019-12-05 13:37:35)
%93% Estimated remaining time(s): 367 (ETA 2019-12-05 13:37:35)
%94% Estimated remaining time(s): 314 (ETA 2019-12-05 13:37:33)
%95% Estimated remaining time(s): 262 (ETA 2019-12-05 13:37:33)
%96% Estimated remaining time(s): 209 (ETA 2019-12-05 13:37:31)
%97% Estimated remaining time(s): 157 (ETA 2019-12-05 13:37:32)
%98% Estimated remaining time(s): 104 (ETA 2019-12-05 13:37:32)
%99% Estimated remaining time(s): 52 (ETA 2019-12-05 13:37:32)
oGetting Null distributions
Path to save analysis_OCDTest/fwe/maxsMinsZ.asc
aPerforming P-correction
oPerforming P-correction
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
Done!
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_OCDTest/OCDTest_z] = [foobin] * [D:/Google]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [D:/Google] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_OCDTest/OCDTest_z] = [foobin] * [D:/Google]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [D:/Google] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir C:\Users\zhuho\sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
Prior open browser
After open browser
o
aCalling MRICron to display 3D results
Mricron call: "C:/Users/zhuho/Documents/win/mricron/mricron.exe" D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/sdm_template.nii.gz -o D:/Google Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_OCDTest/OCDTest_z_p_0.05000_10.nii.gz -o D:/Google Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_OCDTest/OCDTest_z_p_0.05000_10_neg.nii.gz
o
d
I have the same problem. My Os is Windows 10 64. Are there any solutions?
Thanks
Hongru
Home dir C:\Users\zhuho\sdm.conf
Loading study mask gray_matter_2mm
Executing Perm for MyTest with vars ,,, and hyp[1.000000,0.000000,0.000000,0.000000,0.000000]
9 studies included
Using 8 threads
aRecreating studies
file D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/indexes_gray_matter_2mm.bin
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oRecreating studies
aLoading imputations
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oLoading imputations
aGetting Null distributions with 8 threads
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%88% Estimated remaining time(s): 588 (ETA 2019-12-05 11:29:16)
%89% Estimated remaining time(s): 539 (ETA 2019-12-05 11:29:14)
%90% Estimated remaining time(s): 490 (ETA 2019-12-05 11:29:14)
%91% Estimated remaining time(s): 440 (ETA 2019-12-05 11:29:12)
%92% Estimated remaining time(s): 391 (ETA 2019-12-05 11:29:10)
%93% Estimated remaining time(s): 342 (ETA 2019-12-05 11:29:10)
%94% Estimated remaining time(s): 293 (ETA 2019-12-05 11:29:08)
%95% Estimated remaining time(s): 244 (ETA 2019-12-05 11:29:07)
%96% Estimated remaining time(s): 195 (ETA 2019-12-05 11:29:06)
%97% Estimated remaining time(s): 146 (ETA 2019-12-05 11:29:04)
%98% Estimated remaining time(s): 97 (ETA 2019-12-05 11:29:02)
%99% Estimated remaining time(s): 48 (ETA 2019-12-05 11:29:01)
oGetting Null distributions
Path to save analysis_MyTest/fwe/maxsMinsZ.asc
aPerforming P-correction
oPerforming P-correction
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
Done!
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_MyTest/MyTest_z] = [foobin] * [D:/Google]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [D:/Google] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_MyTest/MyTest_z] = [foobin] * [D:/Google]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [D:/Google] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir C:\Users\zhuho\sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
Prior open browser
After open browser
o
aCalling MRICron to display 3D results
Mricron call: "C:/Users/zhuho/Documents/win/mricron/mricron.exe" D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/sdm_template.nii.gz -o D:/Google Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_MyTest/MyTest_z_p_0.05000_10.nii.gz -o D:/Google Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_MyTest/MyTest_z_p_0.05000_10_neg.nii.gz
o
d
getprogdir entry argv D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64/sdm_core
getprogdir exit pdir D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1
Home dir C:\Users\zhuho\sdm.conf
aConducting globals analysis
o
aCalling web browser to display the report
Prior open browser
After open browser
o
d
Home dir C:\Users\zhuho\sdm.conf
Home dir C:\Users\zhuho\sdm.conf
Home dir C:\Users\zhuho\sdm.conf
Load atlas D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/atlas_aal_cts_2mm.nii.gz
length 902629 sdm1_lengt 902629
aAnalyzing coordinates
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o
aCreating anisotropic space
sdm_s_dir got D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\
Path for cor template D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/cor_gray_matter_2mm.nii.gz
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o
aPreprocessing studies
%9% Estimated remaining time(s): 30 (ETA 2019-12-05 11:40:17)
%18% Estimated remaining time(s): 31 (ETA 2019-12-05 11:40:22)
%27% Estimated remaining time(s): 91 (ETA 2019-12-05 11:41:49)
%36% Estimated remaining time(s): 64 (ETA 2019-12-05 11:41:24)
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%72% Estimated remaining time(s): 31 (ETA 2019-12-05 11:41:36)
%81% Estimated remaining time(s): 19 (ETA 2019-12-05 11:41:27)
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
o
aCalling web browser to display the report
Prior open browser
After open browser
o
d
getprogdir entry argv D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64/sdm_core
getprogdir exit pdir D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1
Home dir C:\Users\zhuho\sdm.conf
aConducting globals analysis
o
aCalling web browser to display the report
Prior open browser
After open browser
o
d
Home dir C:\Users\zhuho\sdm.conf
Home dir C:\Users\zhuho\sdm.conf
Home dir C:\Users\zhuho\sdm.conf
Load atlas D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/atlas_aal_cts_2mm.nii.gz
length 902629 sdm1_lengt 902629
aAnalyzing coordinates
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o
aCreating anisotropic space
sdm_s_dir got D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\
Path for cor template D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/cor_gray_matter_2mm.nii.gz
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o
aPreprocessing studies
%9% Estimated remaining time(s): 20 (ETA 2019-12-05 11:52:00)
%18% Estimated remaining time(s): 31 (ETA 2019-12-05 11:52:16)
%27% Estimated remaining time(s): 91 (ETA 2019-12-05 11:53:43)
%36% Estimated remaining time(s): 64 (ETA 2019-12-05 11:53:18)
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%72% Estimated remaining time(s): 31 (ETA 2019-12-05 11:53:31)
%81% Estimated remaining time(s): 19 (ETA 2019-12-05 11:53:22)
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
o
aCalling web browser to display the report
Prior open browser
After open browser
o
d
Home dir C:\Users\zhuho\sdm.conf
iExecuting mle for 'OCDTest' with var1 '' var2 '' var3 '' var4 '' hyp=[1.000000,0.000000,0.000000,0.000000,0.000000] and filter ''
Loading study mask gray_matter_2mm
aStarting MLE...
Using 8 threads
ncoef: 1
aEstimating coefficients...
nLoo: 1
%9% Estimated remaining time(s): 20 (ETA 2019-12-05 11:54:03)
%18% Estimated remaining time(s): 18 (ETA 2019-12-05 11:54:03)
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%90% Estimated remaining time(s): 1 (ETA 2019-12-05 11:53:58)
oEstimating coefficients...
aEstimating tau2...
%1% Estimated remaining time(s): 0 (ETA 2019-12-05 11:53:59)
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oEstimating tau2...
Saving study mask gray_matter_2mm
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incl is 10
dMLE
Loading study mask gray_matter_2mm
iExecuting MI for s_name OCDTest with 50 imputs and filter ''
aStarting MI... with nImputs 50
10 studies included in MI
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Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
dMI
Loading study mask gray_matter_2mm
iRunning meta for OCDTest with var1 '' var2 '' var3 '' var4''
10 studies included in meta
aMeta
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Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
dMeta
Loading study mask gray_matter_2mm
aPool
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a(imgcalc) [analysis_OCDTest/uncorrp.nii.gz] = "1-p values" from "z scores" in [analysis_OCDTest/OCDTest_z.nii.gz]
o
a(imgcalc) [analysis_OCDTest/uncorrp_neg.nii.gz] = 1 - [analysis_OCDTest/uncorrp.nii.gz]
o
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
dPool
Home dir C:\Users\zhuho\sdm.conf
Loading study mask gray_matter_2mm
Executing Perm for OCDTest with vars ,,, and hyp[1.000000,0.000000,0.000000,0.000000,0.000000]
10 studies included
Using 9 threads
aRecreating studies
file D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/indexes_gray_matter_2mm.bin
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oRecreating studies
aLoading imputations
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oLoading imputations
aGetting Null distributions with 9 threads
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oGetting Null distributions
Path to save analysis_OCDTest/fwe/maxsMinsZ.asc
aPerforming P-correction
oPerforming P-correction
Saving study mask gray_matter_2mm
m_mask gray_matter_2mm
Done!
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_OCDTest/OCDTest_z] = [foobin] * [D:/Google]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [D:/Google] = clusters from [foomul] with size >= 10
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
a(imgcalc) [foobin] = [foothr] ? 1 : 0
WARNING: File 'foothr' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_OCDTest/OCDTest_z] = [foobin] * [D:/Google]
WARNING: File 'foobin' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [foomul2] = [foomul] * -1
WARNING: File 'foomul' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
a(imgcalc) [D:/Google] = clusters from [foomul2] with size >= 10
WARNING: File 'foomul2' was not found or is not a NIfTI file (unknown extension).
The program will close as this problem could cause fatal errors.
IMGCALC IMAGE UTILITY (part of the SDM Tools).
http://www.sdmproject.com/sdmtools/imgca...
Syntaxis:
imgcalc [input file] [arguments]
Arguments:
[nothing] # [useful to save as *.nii.gz]
-abs [output file] # y = abs(x)
-acos [output file] # y = acos(x)
-add [input file or number] [output file] # y = x1 + x2
-asin [output file] # y = asin(x)
-atan [output file] # y = atan(x)
-atlas [output file] # [returns blob and atlas info]
-bin [output file] # y = x ? 1 : 0
-blobs [output file] # [returns blob information]
-compl [output file] # y = 1 - x
-cos [output file] # y = cos(x)
-div [input file or number] [output file] # y = x1 / x2
-ethr [number] [output file] # [cluster extent threshold]
-exp [output file] # y = exp(x)
-log [output file] # y = log(x)
-logp2p [output file] # y = 1 - 10^-x
-logp2t [df] [output file] # y = qt(1 - 10^-x, df)
-logp2z [output file] # y = qz(1 - 10^-x)
-mas [input file] [output file] # y = x2 > 0 ? x1 : 0
-max [input file or number] [output file] # y = max(x1, x2)
-min [input file or number] [output file] # y = min(x1, x2)
-mthr [number] [output file] # [cluster mass threshold]
-mul [input file or number] [output file] # y = x1 * x2
-p2logp [output file] # y = -log10(1 - x)
-p2t [df] [output file] # y = qt(x, df)
-p2z [output file] # y = qz(x)
-pow [input file or number] [output file] # y = x1 ^ x2
-pthr [number] [output file] # [cluster peak threshold]
-recip [output file] # y = 1 / x
-rem [input file or number] [output file] # y = x1 % x2
-s [sigma] [output file] # [Gaussian smoothing]
-sdm # [similar to -atlas but for SDM]
-sdmreg [output file] # [linear reg. to SDM template]
-set_logp # [sets values as -log10(p)]
-set_mni # [sets space as MNI]
-set_p # [sets values as 1-p]
-set_t [df] # [sets values as t(df)]
-set_tal # [sets space as Talairach]
-set_z # [sets values as z]
-sin [output file] # y = sin(x)
-sqr [output file] # y = x^2
-sqrt [output file] # y = sqrt(x)
-sub [input file or number] [output file] # y = x1 - x2
-t2logp [output file] # y = -log10(1 - pt(x, df))
-t2p [output file] # y = pt(x, df)
-t2z [output file] # y = qz(pt(x, df))
-tan [output file] # y = tan(x)
-thr [number] [output file] # y = x1 >= x2 ? x1 : 0
-uthr [number] [output file] # y = x1 <= x2 ? x1 : 0
-z2logp [output file] # y = -log10(1 - pz(x))
-z2p [output file] # y = pz(x)
-z2t [df] [output file] # y = qt(pz(x), df)
Home dir C:\Users\zhuho\sdm.conf
aPerforming imgcalc calls
oPerforming imgcalc calls
aCalling web browser to display the report
Prior open browser
After open browser
o
aCalling MRICron to display 3D results
Mricron call: "C:/Users/zhuho/Documents/win/mricron/mricron.exe" D:\Downloads\SdmPsiGui-win64-v6.12\SdmPsiGui-win64-v6.12rc1\bin\windows64\..\..\/share/sdm_template.nii.gz -o D:/Google Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_OCDTest/OCDTest_z_p_0.05000_10.nii.gz -o D:/Google Drive/Onedrive/Documents/paper/meta/pediatric_OCD/OCD/analysis_OCDTest/OCDTest_z_p_0.05000_10_neg.nii.gz
o
d
Dec 17, 2019 01:12 PM | Anton Albajes-Eizagirre - FIDMAG - Germanes Hospitalaries
RE: Problem with preprocessing
Hi, Hongru Zhu,
Could you please describe the commands that you are trying to perform?
Thanks,
Anton
Could you please describe the commands that you are trying to perform?
Thanks,
Anton
Dec 22, 2019 07:12 PM | Hongru Zhu
RE: Problem with preprocessing
Hi Anton,
This error appears when I click the threshold step.
Thanks
Hongru
This error appears when I click the threshold step.
Thanks
Hongru
Jan 7, 2020 11:01 AM | Anton Albajes-Eizagirre - FIDMAG - Germanes Hospitalaries
RE: Problem with preprocessing
Could you please specify the whole command?
for example:
Launched: sdm threshold /home/anton/Documents/testdata/tutorial_newmask/analysis_MyTest_cerebrum/corrp_voxel,/home/anton/Documents/testdata/tutorial_newmask/analysis_MyTest_cerebrum/MyTest_cerebrum_z,0.025,10
Best,
Anton
Originally posted by Hongru Zhu:
for example:
Launched: sdm threshold /home/anton/Documents/testdata/tutorial_newmask/analysis_MyTest_cerebrum/corrp_voxel,/home/anton/Documents/testdata/tutorial_newmask/analysis_MyTest_cerebrum/MyTest_cerebrum_z,0.025,10
Best,
Anton
Originally posted by Hongru Zhu:
Hi Anton,
This error appears when I click the threshold step.
Thanks
Hongru
This error appears when I click the threshold step.
Thanks
Hongru
Feb 19, 2020 04:02 AM | dahlk01
RE: Problem with preprocessing
Hi, for all those having issues thresholding make sure there are no
spaces in the name of your folders for your meta-analyses. I
had this problem and when I changed the space to an underscore I
was able to run the thresholding step without further issue.
Kristina Dahlgren - Emory University
Originally posted by Anton Albajes-Eizagirre:
Kristina Dahlgren - Emory University
Originally posted by Anton Albajes-Eizagirre:
Could you please specify the whole command?
for example:
Launched: sdm threshold /home/anton/Documents/testdata/tutorial_newmask/analysis_MyTest_cerebrum/corrp_voxel,/home/anton/Documents/testdata/tutorial_newmask/analysis_MyTest_cerebrum/MyTest_cerebrum_z,0.025,10
Best,
Anton
Originally posted by Hongru Zhu:
for example:
Launched: sdm threshold /home/anton/Documents/testdata/tutorial_newmask/analysis_MyTest_cerebrum/corrp_voxel,/home/anton/Documents/testdata/tutorial_newmask/analysis_MyTest_cerebrum/MyTest_cerebrum_z,0.025,10
Best,
Anton
Originally posted by Hongru Zhu:
Hi Anton,
This error appears when I click the threshold step.
Thanks
Hongru
This error appears when I click the threshold step.
Thanks
Hongru
Mar 20, 2020 07:03 PM | Anna Kasdan
RE: Problem with preprocessing
Hi all,
Is there a solution for this? I have changed folder names to not include spaces, but am still getting an error with imgcalc in the Threshold step, similar to the previously posted logs. Thank you very much.
Best,
Anna
Is there a solution for this? I have changed folder names to not include spaces, but am still getting an error with imgcalc in the Threshold step, similar to the previously posted logs. Thank you very much.
Best,
Anna