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