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: on behalf of "Yendiki,
Anastasia"
Reply-To: Freesurfer support list
Date: Thursday, October 21, 2021 at 5:06 PM
To: "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-boun...@nmr.mgh.harvard.edu
on behalf of Chong, Catherine (Cat),
Ph.D.
Sent: Thursday, October 21, 2021 6:16 PM
To: 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> [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 : only use volume from each input file (first volume is 0 not 1)
Usage: fslmerge <-x/y/z/t/a/tr> [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 : only use volume 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_.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_.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
