Hi Bahram - Can you please send us your entire trac-all.log file? Thanks!
a.y On Fri, 14 Aug 2015, B M wrote:
Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected Could you please advise me what to do? Best Bahram
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