Not sure why, could be a specific version of FSL. You can try running the step
that merges everything separately:
bedpostx_postproc.sh /path/to/your/tracula/dir/subjname/dmri
On a separate note: I have to do some emergency travel so I will not be
monitoring the list through the next week.
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Chong, Catherine (Cat),
Ph.D. <chong.cather...@mayo.edu>
Sent: Thursday, October 21, 2021 6:16 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Dracula 7.2 -bedp error
External Email - Use Caution
Dear Tracula team,
I am running 7.2 on a computing cluster and the -prep stage completes without
error. The dmri directory show the following files, below.
However, after running the second step ( -bedp), the files under dmri.bedpostX
do not appear to have merged.
(bvals bvecs cancel commands.txt diff_slices logs monitor xfms). I am
not able to find any error messages and the bedpostx_post.o529573 log is below.
I have also attached my script to the very bottom.
I would be grateful for your guidance in helping me solve this problem.
Cat
Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in
seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final
option value
-n <N> : only use volume <N> from each input file (first volume is 0 not 1)
Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in
seconds]
-t : concatenate images in time
-x : concatenate images in the x direction
-y : concatenate images in the y direction
-z : concatenate images in the z direction
-a : auto-choose: single slices -> volume, volumes -> 4D (time series)
-tr : concatenate images in time and set the output image tr to the final
option value
-n <N> : only use volume <N> from each input file (first volume is 0 not 1)
Removing intermediate files
Creating identity xfm
Done
~
brain_anat_mni.nii.gz data_slice_0018.nii.gz data_slice_0042.nii.gz
dcminfo.dat lowb_brain.nii.gz
nodif_brain_mask_slice_0021.nii.gz nodif_brain_mask_slice_0045.nii.gz
brain_anat.nii.gz data_slice_0019.nii.gz data_slice_0043.nii.gz
dtifit_FA.nii.gz lowb.nii.gz
nodif_brain_mask_slice_0022.nii.gz nodif_brain_mask_slice_0046.nii.gz
brain_anat_orig.nii.gz data_slice_0020.nii.gz data_slice_0044.nii.gz
dtifit_L1.nii.gz nodif_brain_mask.nii.gz
nodif_brain_mask_slice_0023.nii.gz nodif_brain_mask_slice_0047.nii.gz
bvals data_slice_0021.nii.gz data_slice_0045.nii.gz
dtifit_L2.nii.gz nodif_brain_mask_slice_0000.nii.gz
nodif_brain_mask_slice_0024.nii.gz nodif_brain_mask_slice_0048.nii.gz
bvecs data_slice_0022.nii.gz data_slice_0046.nii.gz
dtifit_L3.nii.gz nodif_brain_mask_slice_0001.nii.gz
nodif_brain_mask_slice_0025.nii.gz nodif_brain_mask_slice_0049.nii.gz
data.nii.gz data_slice_0023.nii.gz data_slice_0047.nii.gz
dtifit_MD.nii.gz nodif_brain_mask_slice_0002.nii.gz
nodif_brain_mask_slice_0026.nii.gz nodif_brain_mask_slice_0050.nii.gz
data_slice_0000.nii.gz data_slice_0024.nii.gz data_slice_0048.nii.gz
dtifit_MO.nii.gz nodif_brain_mask_slice_0003.nii.gz
nodif_brain_mask_slice_0027.nii.gz nodif_brain_mask_slice_0051.nii.gz
data_slice_0001.nii.gz data_slice_0025.nii.gz data_slice_0049.nii.gz
dtifit_S0.nii.gz nodif_brain_mask_slice_0004.nii.gz
nodif_brain_mask_slice_0028.nii.gz nodif_brain_mask_slice_0052.nii.gz
data_slice_0002.nii.gz data_slice_0026.nii.gz data_slice_0050.nii.gz
dtifit_V1.nii.gz nodif_brain_mask_slice_0005.nii.gz
nodif_brain_mask_slice_0029.nii.gz nodif_brain_mask_slice_0053.nii.gz
data_slice_0003.nii.gz data_slice_0027.nii.gz data_slice_0051.nii.gz
dtifit_V2.nii.gz nodif_brain_mask_slice_0006.nii.gz
nodif_brain_mask_slice_0030.nii.gz nodif_brain_mask_slice_0054.nii.gz
data_slice_0004.nii.gz data_slice_0028.nii.gz data_slice_0052.nii.gz
dtifit_V3.nii.gz nodif_brain_mask_slice_0007.nii.gz
nodif_brain_mask_slice_0031.nii.gz nodif_brain_mask_slice_0055.nii.gz
data_slice_0005.nii.gz data_slice_0029.nii.gz data_slice_0053.nii.gz
dwi.bvals nodif_brain_mask_slice_0008.nii.gz
nodif_brain_mask_slice_0032.nii.gz nodif_brain_mask_slice_0056.nii.gz
data_slice_0006.nii.gz data_slice_0030.nii.gz data_slice_0054.nii.gz
dwi.bvecs nodif_brain_mask_slice_0009.nii.gz
nodif_brain_mask_slice_0033.nii.gz nodif_brain_mask_slice_0057.nii.gz
data_slice_0007.nii.gz data_slice_0031.nii.gz data_slice_0055.nii.gz
dwi.ecclog nodif_brain_mask_slice_0010.nii.gz
nodif_brain_mask_slice_0034.nii.gz nodif_brain_mask_slice_0058.nii.gz
data_slice_0008.nii.gz data_slice_0032.nii.gz data_slice_0056.nii.gz
dwi_motion_byvol.txt nodif_brain_mask_slice_0011.nii.gz
nodif_brain_mask_slice_0035.nii.gz nodif_brain_mask_slice_0059.nii.gz
data_slice_0009.nii.gz data_slice_0033.nii.gz data_slice_0057.nii.gz
dwi_motion.txt nodif_brain_mask_slice_0012.nii.gz
nodif_brain_mask_slice_0036.nii.gz nodif_brain_mask_slice_0060.nii.gz
data_slice_0010.nii.gz data_slice_0034.nii.gz data_slice_0058.nii.gz
dwi.nii.gz nodif_brain_mask_slice_0013.nii.gz
nodif_brain_mask_slice_0037.nii.gz nodif_brain_mask_slice_0061.nii.gz
data_slice_0011.nii.gz data_slice_0035.nii.gz data_slice_0059.nii.gz
dwi_orig.1.bvals nodif_brain_mask_slice_0014.nii.gz
nodif_brain_mask_slice_0038.nii.gz nodif_brain_mask_slice_0062.nii.gz
data_slice_0012.nii.gz data_slice_0036.nii.gz data_slice_0060.nii.gz
dwi_orig.1.bvecs nodif_brain_mask_slice_0015.nii.gz
nodif_brain_mask_slice_0039.nii.gz nodif_brain_mask_slice_0063.nii.gz
data_slice_0013.nii.gz data_slice_0037.nii.gz data_slice_0061.nii.gz
dwi_orig.1.nii.gz nodif_brain_mask_slice_0016.nii.gz
nodif_brain_mask_slice_0040.nii.gz nodif_brain_mask_slice_0064.nii.gz
data_slice_0014.nii.gz data_slice_0038.nii.gz data_slice_0062.nii.gz
dwi_orig_las.bvals nodif_brain_mask_slice_0017.nii.gz
nodif_brain_mask_slice_0041.nii.gz nodif_brain_mask_slice_0065.nii.gz
data_slice_0015.nii.gz data_slice_0039.nii.gz data_slice_0063.nii.gz
dwi_orig_las.bvecs nodif_brain_mask_slice_0018.nii.gz
nodif_brain_mask_slice_0042.nii.gz xfms
data_slice_0016.nii.gz data_slice_0040.nii.gz data_slice_0064.nii.gz
dwi_orig_las.nii.gz nodif_brain_mask_slice_0019.nii.gz
nodif_brain_mask_slice_0043.nii.gz
data_slice_0017.nii.gz data_slice_0041.nii.gz data_slice_0065.nii.gz
dwi_snr.txt nodif_brain_mask_slice_0020.nii.gz
nodif_brain_mask_slice_0044.nii.gz
! /bin/bash
#$ -N recon-all
#$ -cwd
#$ -o /research/ freesurfer/logs_$TASK_ID
#$ -e /research/ /freesurfer/logs_$TASK_ID
#$ -j y
#$ -M x...@mayo.edu
#$ -m abe
###$ -pe threaded 4
#$ -notify
#$ -l h_vmem=20G
#$ -V
#$ -l h_stack=20M
#$ -t 1
set -x
curr_subj=$(sed -n "${SGE_TASK_ID}p"
/research/labs/neurology/cat/freesurfer/subjects/subject_list3)
echo $curr_subj
export FREESURFER_HOME=/usr/local/biotools/freesurfer/freesurfer-v7.2.0
export SUBJECTS_DIR=/research/labs/neurology/cat/freesurfer/subjects
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export FSLDIR="/usr/local/biotools/fsl/6.0.5/"
source ${FSLDIR}/etc/fslconf/fsl.sh
export PATH="${FSLDIR}/bin:${FREESURFER_HOME}/bin:$PATH"
export FSLDIR PATH
unset PROFILE
cat > config << END
set dtroot = $SUBJECTS_DIR/Tracula
set subjlist = DODHC09_1_out
set dcmroot = $SUBJECTS_DIR/$curr_subj
set dob0 = 0
set doeddy = 1
set interreg = 1
END
trac-all -path -i $SUBJECTS_DIR/$curr_subj/IM-0003-0001.dcm -subject
${curr_subj} -c config
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