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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 xx@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