Hi Bahram - The anatomical-to-diffusion registration matrix is all zeros,
so something went wrong there. I'll need to see all the output files to
investigate. Can you please zip up this subject's tracula output
directories (dmri, dmri.bedpostX, dpath, dlabel, scripts) and upload
everything for me here?
https://gate.nmr.mgh.harvard.edu/filedrop2/
Thanks,
a.y
On Thu, 20 Aug 2015, B M wrote:
Hi Anastasia,
please find the files in attachment.
Best regards
Bahram
2015-08-19 21:55 GMT+02:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>:
Hi Bahram - There are some errors in there related to registration files.
Can you please send these files?
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat
bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat
Thanks,
a.y
On Tue, 18 Aug 2015, B M wrote:
Hi Anastasia,
Please find attached the trac-all.log file. Thank you very much for
your help.
Bahram
2015-08-17 19:31 GMT+02:00 Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>:
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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