sdm-help-list > RE: Problem with preprocessing
Dec 5, 2019  01:12 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)
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%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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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)
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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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%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)
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%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)
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%85% Estimated remaining time(s): 115 (ETA 2019-12-05 12:07:14)
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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
%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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oRecreating studies
aLoading imputations
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oLoading imputations
aGetting Null distributions with 9 threads
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%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

Threaded View

TitleAuthorDate
Tinya Chang Aug 14, 2019
Anna Kasdan Mar 20, 2020
Anton Albajes-Eizagirre Nov 26, 2019
Rebecca Hu Sep 12, 2019
Rebecca Hu Sep 12, 2019
e0046902 Nov 3, 2019
Arnaud Leroy Nov 19, 2019
Anton Albajes-Eizagirre Aug 16, 2019
Brandon Gunasekera Sep 3, 2019
RE: Problem with preprocessing
Hongru Zhu Dec 5, 2019
Anton Albajes-Eizagirre Dec 17, 2019
Hongru Zhu Dec 22, 2019
Anton Albajes-Eizagirre Jan 7, 2020
dahlk01 Feb 18, 2020