open-discussion > Problems with FDT-bedpostx
Showing 1-5 of 5 posts
Sep 18, 2017 04:09 AM | Mir Jeong
Problems with FDT-bedpostx
Hello, I'm attempting to use FDT of FSL.
I have successfully used the 'dtifit' command.
I've encountered some problems when trying to use 'bedpostx'
(FSL-FDT diffusion-BEDPOSTX Estimation of diffusion parameters)
I tried to use the input directory as:
/home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/
(with advanced options: Fibres-2, Weight-1, Burn In-1000)
When I hit go, 'Errors: child process exited abnormally' message pops up.
bedpostx /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/. --nf=2 --fudge=1 --bi=1000
/usr/share/fsl/5.0/bin/bedpostx /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/. --nf=2 --fudge=1 --bi=1000
subjectdir is /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474
/home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data not found
Here's the list of files I have.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474$ ls
20080811_204605ACEprotocol415088s009a1001.bval
20080811_204605ACEprotocol415088s009a1001.bvec
20080811_204605ACEprotocol415088s009a1001.nii.gz
20080811_204605ACEprotocol415088s009a1001_eddy.ecclog
20080811_204605ACEprotocol415088s009a1001_eddy.nii.gz
DTI_FA.nii.gz
DTI_L1.nii.gz
DTI_L2.nii.gz
DTI_L3.nii.gz
DTI_MD.nii.gz
DTI_MO.nii.gz
DTI_S0.nii.gz
DTI_V1.nii.gz
DTI_V2.nii.gz
DTI_V3.nii.gz
b0.nii.gz
b0_brain.nii.gz
b0_brain_mask.nii.gz
bedpostcom_log.tcl
I would appreciate it if someone pinpoints the problem and how to fix it.
I have successfully used the 'dtifit' command.
I've encountered some problems when trying to use 'bedpostx'
(FSL-FDT diffusion-BEDPOSTX Estimation of diffusion parameters)
I tried to use the input directory as:
/home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/
(with advanced options: Fibres-2, Weight-1, Burn In-1000)
When I hit go, 'Errors: child process exited abnormally' message pops up.
bedpostx /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/. --nf=2 --fudge=1 --bi=1000
/usr/share/fsl/5.0/bin/bedpostx /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/. --nf=2 --fudge=1 --bi=1000
subjectdir is /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474
/home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data not found
Here's the list of files I have.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474$ ls
20080811_204605ACEprotocol415088s009a1001.bval
20080811_204605ACEprotocol415088s009a1001.bvec
20080811_204605ACEprotocol415088s009a1001.nii.gz
20080811_204605ACEprotocol415088s009a1001_eddy.ecclog
20080811_204605ACEprotocol415088s009a1001_eddy.nii.gz
DTI_FA.nii.gz
DTI_L1.nii.gz
DTI_L2.nii.gz
DTI_L3.nii.gz
DTI_MD.nii.gz
DTI_MO.nii.gz
DTI_S0.nii.gz
DTI_V1.nii.gz
DTI_V2.nii.gz
DTI_V3.nii.gz
b0.nii.gz
b0_brain.nii.gz
b0_brain_mask.nii.gz
bedpostcom_log.tcl
I would appreciate it if someone pinpoints the problem and how to fix it.
Sep 18, 2017 05:09 PM | Sulantha Sanjeewa
Problems with FDT-bedpostx
> Just a shot in the dark, what happens if you create a data
folder inside
> /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/N
> DARupload/NDAR_upload_SN/ndar_DTI51_data/s797474 and move all your input
> files into it ?
>
> /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/N
> DARupload/NDAR_upload_SN/ndar_DTI51_data/s797474 and move all your input
> files into it ?
>
Sep 19, 2017 12:09 PM | Cheol Han
RE: Problems with FDT-bedpostx
Hello,
The filenames are important. BedpostX requires a folder which contains following files. (see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide)
Input directory: Use the browse button to select an input directory. That directory must contain the following files:
data: A 4D series of data volumes. This will include diffusion-weighted volumes and volume(s) with no diffusion weighting.
nodif_brain_mask: 3D binary brain mask volume derived from running bet on nodif (i.e. on a volume with no diffusion weighting).
bvecs (with no file extension): An ASCII text file containing a list of gradient directions applied during diffusion weighted volumes. The order of entries in this file must match the order of volumes in data.
First, rename filenames through the following commands.
cp 20080811_204605ACEprotocol415088s009a1001_eddy.nii.gz data.nii.gz
cp b0_brain_mask.nii.gz nodif_brain_mask
Second, bvec processing. Did you use "fdt_rotate_bvecs"?
I think that you performed the eddy current correction on the image but did not perform the bvec correction.
if you rotate the bvecs, just type as follows.
cp 20080811_204605ACEprotocol415088s009a1001.bvec bvecs
If not, type the following lines.
fdt_rotate_bvecs 20080811_204605ACEprotocol415088s009a1001.bvec bvecs 20080811_204605ACEprotocol415088s009a1001_eddy.ecclog
I hope this helps.
Best
Cheol
The filenames are important. BedpostX requires a folder which contains following files. (see https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide)
Input directory: Use the browse button to select an input directory. That directory must contain the following files:
data: A 4D series of data volumes. This will include diffusion-weighted volumes and volume(s) with no diffusion weighting.
nodif_brain_mask: 3D binary brain mask volume derived from running bet on nodif (i.e. on a volume with no diffusion weighting).
bvecs (with no file extension): An ASCII text file containing a list of gradient directions applied during diffusion weighted volumes. The order of entries in this file must match the order of volumes in data.
First, rename filenames through the following commands.
cp 20080811_204605ACEprotocol415088s009a1001_eddy.nii.gz data.nii.gz
cp b0_brain_mask.nii.gz nodif_brain_mask
Second, bvec processing. Did you use "fdt_rotate_bvecs"?
I think that you performed the eddy current correction on the image but did not perform the bvec correction.
if you rotate the bvecs, just type as follows.
cp 20080811_204605ACEprotocol415088s009a1001.bvec bvecs
If not, type the following lines.
fdt_rotate_bvecs 20080811_204605ACEprotocol415088s009a1001.bvec bvecs 20080811_204605ACEprotocol415088s009a1001_eddy.ecclog
I hope this helps.
Best
Cheol
Sep 21, 2017 12:09 AM | Mir Jeong
RE: Problems with FDT-bedpostx
Thanks for helping me.
However, I still have a problem.
I followed your advice.
I created a new directory named 'data' and put 'data.nii.gz', 'nodif_brain_mask', and 'bvecs' into it.
However, when I tried to rotate the bvecs, something feels wrong with the message: 'unexpected operator' , 'not found'.
I think the bvecs rotation didn't work correctly.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data$ /usr/lib/fsl/5.0/bedpostx_datacheck ../data
../data/data
data_type INT16
dim1 128
dim2 128
dim3 47
dim4 52
datatype 4
pixdim1 1.875000
pixdim2 1.875000
pixdim3 2.500025
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
../data/nodif_brain_mask
data_type INT16
dim1 128
dim2 128
dim3 47
dim4 1
datatype 4
pixdim1 1.875000
pixdim2 1.875000
pixdim3 2.500025
pixdim4 1.000000
cal_max 1.0000
cal_min 0.0000
file_type NIFTI-1+
num lines in ../data/bvals
1
num words in ../data/bvals
52
num lines in ../data/bvecs
3
num words in ../data/bvecs
3
bvecs and bvals are incompatible
number of vectors in bvecs is not equal to number of vols in data
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474$ fdt_rotate_bvecs 20080811_204605ACEprotocol415088s009a1001.bvec bvecs 20080811_204605ACEprotocol415088s009a1001_eddy.ecclog
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 3: [: 20080811_204605ACEprotocol415088s009a1001_eddy.ecclog: unexpected operator
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0000: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0001: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0002: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0003: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0004: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0005: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0006: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0007: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0008: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0009: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0010: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0011: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0012: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0013: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0014: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0015: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0016: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0017: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0018: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0019: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0020: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0021: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0022: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0023: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0024: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0025: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0026: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0027: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0028: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0029: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0030: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0031: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0032: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0033: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0034: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0035: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0036: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0037: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0038: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0039: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0040: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0041: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0042: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0043: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0044: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0045: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0046: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0047: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0048: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0049: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0050: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0051: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
I tried to use the input directory as:
/home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data/*
(with advanced options: Fibres-2, Weight-1, Burn In-1000)
(By the way, I also needed 'bvals' in order to run BEDPOSTX)
When I hit go, it seemed to work fine at first, but then
'Errors: child killed: kill signal' popped up.
I wonder what the problem is now.
switching from /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data to /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data
bedpostx /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data/. --nf=2 --fudge=1 --bi=1000
/usr/share/fsl/5.0/bin/bedpostx /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data/. --nf=2 --fudge=1 --bi=1000
subjectdir is /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
----- Bedpostx Monitor -----
Queuing post processing stage
An error ocurred. Please check file /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data.bedpostX/logs/bedpostx.e7493.1
I've obtained the following files in ~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data:
bedpostcom_log.tcl
data_slice_0000.nii.gz ~ data_slice_0046.nii.gz
nodif_brain_mask_slice_0000.nii.gz ~ nodif_brain_mask_slice_0046.nii.gz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data.bedpostX$ ls
bvals bvecs commands.txt diff_slices logs monitor nodif_brain_mask.nii.gz xfms
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data.bedpostX/logs$ ls
bedpostx.e7493.1 bedpostx.e7493.20 bedpostx.e7493.31 bedpostx.e7493.42 bedpostx.o7493.10 bedpostx.o7493.21 bedpostx.o7493.32 bedpostx.o7493.43 bpx_preproc.e5763 log0010 log0022 log0034 log0046
bedpostx.e7493.10 bedpostx.e7493.21 bedpostx.e7493.32 bedpostx.e7493.43 bedpostx.o7493.11 bedpostx.o7493.22 bedpostx.o7493.33 bedpostx.o7493.44 bpx_preproc.o5763 log0011 log0023 log0035 monitor
bedpostx.e7493.11 bedpostx.e7493.22 bedpostx.e7493.33 bedpostx.e7493.44 bedpostx.o7493.12 bedpostx.o7493.23 bedpostx.o7493.34 bedpostx.o7493.45 log0000 log0012 log0024 log0036 postproc_ID
bedpostx.e7493.12 bedpostx.e7493.23 bedpostx.e7493.34 bedpostx.e7493.45 bedpostx.o7493.13 bedpostx.o7493.24 bedpostx.o7493.35 bedpostx.o7493.46 log0001 log0013 log0025 log0037
bedpostx.e7493.13 bedpostx.e7493.24 bedpostx.e7493.35 bedpostx.e7493.46 bedpostx.o7493.14 bedpostx.o7493.25 bedpostx.o7493.36 bedpostx.o7493.47 log0002 log0014 log0026 log0038
bedpostx.e7493.14 bedpostx.e7493.25 bedpostx.e7493.36 bedpostx.e7493.47 bedpostx.o7493.15 bedpostx.o7493.26 bedpostx.o7493.37 bedpostx.o7493.5 log0003 log0015 log0027 log0039
bedpostx.e7493.15 bedpostx.e7493.26 bedpostx.e7493.37 bedpostx.e7493.5 bedpostx.o7493.16 bedpostx.o7493.27 bedpostx.o7493.38 bedpostx.o7493.6 log0004 log0016 log0028 log0040
bedpostx.e7493.16 bedpostx.e7493.27 bedpostx.e7493.38 bedpostx.e7493.6 bedpostx.o7493.17 bedpostx.o7493.28 bedpostx.o7493.39 bedpostx.o7493.7 log0005 log0017 log0029 log0041
bedpostx.e7493.17 bedpostx.e7493.28 bedpostx.e7493.39 bedpostx.e7493.7 bedpostx.o7493.18 bedpostx.o7493.29 bedpostx.o7493.4 bedpostx.o7493.8 log0006 log0018 log0030 log0042
bedpostx.e7493.18 bedpostx.e7493.29 bedpostx.e7493.4 bedpostx.e7493.8 bedpostx.o7493.19 bedpostx.o7493.3 bedpostx.o7493.40 bedpostx.o7493.9 log0007 log0019 log0031 log0043
bedpostx.e7493.19 bedpostx.e7493.3 bedpostx.e7493.40 bedpostx.e7493.9 bedpostx.o7493.2 bedpostx.o7493.30 bedpostx.o7493.41 bpx_postproc.e8264 log0008 log0020 log0032 log0044
bedpostx.e7493.2 bedpostx.e7493.30 bedpostx.e7493.41 bedpostx.o7493.1 bedpostx.o7493.20 bedpostx.o7493.31 bedpostx.o7493.42 bpx_postproc.o8264 log0009 log0021 log0033 log0045
Looking at the logs
~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data.bedpostX/logs$ cat bedpostx.e7493.1
An exception has been thrown
Logic error:- detected by Newmat: index error: requested index = 2
MatrixType = Rect # Rows = 1; # Cols = 1
I wonder what the error message means and how I can solve it.
However, I still have a problem.
I followed your advice.
I created a new directory named 'data' and put 'data.nii.gz', 'nodif_brain_mask', and 'bvecs' into it.
However, when I tried to rotate the bvecs, something feels wrong with the message: 'unexpected operator' , 'not found'.
I think the bvecs rotation didn't work correctly.
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data$ /usr/lib/fsl/5.0/bedpostx_datacheck ../data
../data/data
data_type INT16
dim1 128
dim2 128
dim3 47
dim4 52
datatype 4
pixdim1 1.875000
pixdim2 1.875000
pixdim3 2.500025
pixdim4 1.000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
../data/nodif_brain_mask
data_type INT16
dim1 128
dim2 128
dim3 47
dim4 1
datatype 4
pixdim1 1.875000
pixdim2 1.875000
pixdim3 2.500025
pixdim4 1.000000
cal_max 1.0000
cal_min 0.0000
file_type NIFTI-1+
num lines in ../data/bvals
1
num words in ../data/bvals
52
num lines in ../data/bvecs
3
num words in ../data/bvecs
3
bvecs and bvals are incompatible
number of vectors in bvecs is not equal to number of vols in data
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474$ fdt_rotate_bvecs 20080811_204605ACEprotocol415088s009a1001.bvec bvecs 20080811_204605ACEprotocol415088s009a1001_eddy.ecclog
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 3: [: 20080811_204605ACEprotocol415088s009a1001_eddy.ecclog: unexpected operator
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0000: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0001: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0002: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0003: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0004: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0005: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0006: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0007: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0008: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0009: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0010: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0011: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0012: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0013: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0014: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0015: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0016: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0017: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0018: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0019: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0020: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0021: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0022: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0023: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0024: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0025: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0026: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0027: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0028: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0029: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0030: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0031: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0032: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0033: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0034: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0035: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0036: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0037: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0038: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0039: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0040: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0041: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0042: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0043: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0044: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0045: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0046: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0047: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0048: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0049: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0050: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
1
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 29: [: processing 20080811_204605ACEprotocol415088s009a1001_eddy_tmp0051: unexpected operator
/usr/lib/fsl/5.0/fdt_rotate_bvecs: 67: /usr/lib/fsl/5.0/fdt_rotate_bvecs: let: not found
I tried to use the input directory as:
/home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data/*
(with advanced options: Fibres-2, Weight-1, Burn In-1000)
(By the way, I also needed 'bvals' in order to run BEDPOSTX)
When I hit go, it seemed to work fine at first, but then
'Errors: child killed: kill signal' popped up.
I wonder what the problem is now.
switching from /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data to /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data
bedpostx /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data/. --nf=2 --fudge=1 --bi=1000
/usr/share/fsl/5.0/bin/bedpostx /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data/. --nf=2 --fudge=1 --bi=1000
subjectdir is /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
----- Bedpostx Monitor -----
Queuing post processing stage
An error ocurred. Please check file /home/eternal/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data.bedpostX/logs/bedpostx.e7493.1
I've obtained the following files in ~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data:
bedpostcom_log.tcl
data_slice_0000.nii.gz ~ data_slice_0046.nii.gz
nodif_brain_mask_slice_0000.nii.gz ~ nodif_brain_mask_slice_0046.nii.gz
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data.bedpostX$ ls
bvals bvecs commands.txt diff_slices logs monitor nodif_brain_mask.nii.gz xfms
eternal@DESKTOP-UNTM4IS:~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data.bedpostX/logs$ ls
bedpostx.e7493.1 bedpostx.e7493.20 bedpostx.e7493.31 bedpostx.e7493.42 bedpostx.o7493.10 bedpostx.o7493.21 bedpostx.o7493.32 bedpostx.o7493.43 bpx_preproc.e5763 log0010 log0022 log0034 log0046
bedpostx.e7493.10 bedpostx.e7493.21 bedpostx.e7493.32 bedpostx.e7493.43 bedpostx.o7493.11 bedpostx.o7493.22 bedpostx.o7493.33 bedpostx.o7493.44 bpx_preproc.o5763 log0011 log0023 log0035 monitor
bedpostx.e7493.11 bedpostx.e7493.22 bedpostx.e7493.33 bedpostx.e7493.44 bedpostx.o7493.12 bedpostx.o7493.23 bedpostx.o7493.34 bedpostx.o7493.45 log0000 log0012 log0024 log0036 postproc_ID
bedpostx.e7493.12 bedpostx.e7493.23 bedpostx.e7493.34 bedpostx.e7493.45 bedpostx.o7493.13 bedpostx.o7493.24 bedpostx.o7493.35 bedpostx.o7493.46 log0001 log0013 log0025 log0037
bedpostx.e7493.13 bedpostx.e7493.24 bedpostx.e7493.35 bedpostx.e7493.46 bedpostx.o7493.14 bedpostx.o7493.25 bedpostx.o7493.36 bedpostx.o7493.47 log0002 log0014 log0026 log0038
bedpostx.e7493.14 bedpostx.e7493.25 bedpostx.e7493.36 bedpostx.e7493.47 bedpostx.o7493.15 bedpostx.o7493.26 bedpostx.o7493.37 bedpostx.o7493.5 log0003 log0015 log0027 log0039
bedpostx.e7493.15 bedpostx.e7493.26 bedpostx.e7493.37 bedpostx.e7493.5 bedpostx.o7493.16 bedpostx.o7493.27 bedpostx.o7493.38 bedpostx.o7493.6 log0004 log0016 log0028 log0040
bedpostx.e7493.16 bedpostx.e7493.27 bedpostx.e7493.38 bedpostx.e7493.6 bedpostx.o7493.17 bedpostx.o7493.28 bedpostx.o7493.39 bedpostx.o7493.7 log0005 log0017 log0029 log0041
bedpostx.e7493.17 bedpostx.e7493.28 bedpostx.e7493.39 bedpostx.e7493.7 bedpostx.o7493.18 bedpostx.o7493.29 bedpostx.o7493.4 bedpostx.o7493.8 log0006 log0018 log0030 log0042
bedpostx.e7493.18 bedpostx.e7493.29 bedpostx.e7493.4 bedpostx.e7493.8 bedpostx.o7493.19 bedpostx.o7493.3 bedpostx.o7493.40 bedpostx.o7493.9 log0007 log0019 log0031 log0043
bedpostx.e7493.19 bedpostx.e7493.3 bedpostx.e7493.40 bedpostx.e7493.9 bedpostx.o7493.2 bedpostx.o7493.30 bedpostx.o7493.41 bpx_postproc.e8264 log0008 log0020 log0032 log0044
bedpostx.e7493.2 bedpostx.e7493.30 bedpostx.e7493.41 bedpostx.o7493.1 bedpostx.o7493.20 bedpostx.o7493.31 bedpostx.o7493.42 bpx_postproc.o8264 log0009 log0021 log0033 log0045
Looking at the logs
~/c9image/NDARAF706DLN/s797474/ace/data/NDARupload/NDAR_upload_SN/ndar_DTI51_data/s797474/data.bedpostX/logs$ cat bedpostx.e7493.1
An exception has been thrown
Logic error:- detected by Newmat: index error: requested index = 2
MatrixType = Rect # Rows = 1; # Cols = 1
I wonder what the error message means and how I can solve it.
Oct 9, 2017 03:10 PM | Cheol Han
RE: Problems with FDT-bedpostx
Hi
I am sorry for the late reply (it was a long holiday in Korea)
I. rotating bvecs
You're in a wrong directory. In the directory you typed "fdt_rotate" does not contain the ecc log file.
What you should do is..
1. rotate bvec in the original directory
2. make a new folder "data"
3. copy the data.nii.gz (eddy corrected one.) into the data directory
4. copy the rotated bvecs and bvals into the data directory
5. copy the nodif_brain_mask into the data directory.
6. make sure all names are apppropriate (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/F...)
ii. bedpostx
I think you did not perform dtifit...
please follow https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide
Best
Cheol
I am sorry for the late reply (it was a long holiday in Korea)
I. rotating bvecs
You're in a wrong directory. In the directory you typed "fdt_rotate" does not contain the ecc log file.
What you should do is..
1. rotate bvec in the original directory
2. make a new folder "data"
3. copy the data.nii.gz (eddy corrected one.) into the data directory
4. copy the rotated bvecs and bvals into the data directory
5. copy the nodif_brain_mask into the data directory.
6. make sure all names are apppropriate (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/F...)
ii. bedpostx
I think you did not perform dtifit...
please follow https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide
Best
Cheol