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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
