Re: [Freesurfer] [EXTERNAL] Re: Tracula 7.2 -bedp error

External Email - Use Caution

Dear Tracula Team, I ran the command suggested below to merge the files: bedpostx_postproc.sh /path/to/your/tracula/dir/subjname/dmri But this did not seem to work unfortunately, here is the output.

Removing intermediate files

Creating identity xfm

/usr/local/biotools/fsl/6.0.5/bin/bedpostx_postproc.sh: line 150: /research/labs/neurology/cat/freesurfer/subjects/Tracula/DODHC09_1_out/dmri.bedpostX.bedpostX/xfms/eye.mat: No such file or directory

/usr/local/biotools/fsl/6.0.5/bin/bedpostx_postproc.sh: line 151: /research/labs/neurology/cat/freesurfer/subjects/Tracula/DODHC09_1_out/dmri.bedpostX.bedpostX/xfms/eye.mat: No such file or directory

/usr/local/biotools/fsl/6.0.5/bin/bedpostx_postproc.sh: line 152: /research/labs/neurology/cat/freesurfer/subjects/Tracula/DODHC09_1_out/dmri.bedpostX.bedpostX/xfms/eye.mat: No such file or directory

/usr/local/biotools/fsl/6.0.5/bin/bedpostx_postproc.sh: line 153: /research/labs/neurology/cat/freesurfer/subjects/Tracula/DODHC09_1_out/dmri.bedpostX.bedpostX/xfms/eye.mat: No such file or directory

Done

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, October 21, 2021 at 5:06 PM To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] Dracula 7.2 -bedp error

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Chong, Catherine (Cat), Ph.D. Chong.Catherine@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 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