Thanks for your quick and helpful answer. I hope your server doesn’t treat me like SPAM already. ;-)
Anyways I have some several other questions. Is there a way to run bedpostX for different subjects in a row? Or do I have to run it for each subject separately. I’m a Linux-newbie, so I’m not familiar with writing own scripts.
I’m currently testing Tracula on our MRI-computer, but in the near future we will try to get Tracula working on the cluster (as we are doing already for recon-all). Is there a way to solve the error that occurs when running bedpostX through the trac-all command (see below)?
I’m also getting the following error when running bedpostX directly:
../dmri.bedpostX/monitor: Permission denied.
I see that there are still files produced by the command, so I think I shouldn’t give this error a lot of attention? I’ve already tried to adjust the permission in my SUBJECTS_DIR with the recursive option -R (chmod a+rwx -R $SUBJECTS_DIR), but this doesn’t seem to fix the problem.
Thanks for the already given advice,
Regards,
Robby
Robby De Pauw, drs.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent
Hi Robby - Since you're running it locally and not on a cluster, you can
just run bedpostx directly:
bedpostx /media/mri/DATAPART11/ROBBY/FREESURFER/T1/INP_080_LISA_V_1/dmri
a.y
On Tue, 9 Sep 2014, Robby De Pauw wrote:
Dear Anastasia, Barbara & FS-community,
The preprocessing step of Tracula was succesfully completed. However
when I try to do the next step: fitting the Ball & Stick model I get
another error:
mri@ge24c165:/media/mri/DATAPART11/ROBBY/FREESURFER$ trac-all -bedp -c
dmrirc.info
INFO: SUBJECTS_DIR is /media/mri/DATAPART11/ROBBY/FREESURFER/T1
INFO: Diffusion root is /media/mri/DATAPART11/ROBBY/FREESURFER/T1
Actual FREESURFER_HOME /usr/local/freesurfer
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous:
/apps/gent/SL6/sandybridge/software/FreeSurfer/5.3.0-centos4_x86_64
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
/media/mri/DATAPART11/ROBBY/FREESURFER/T1/INP_080_LISA_V_1/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected
I have already searched through your mailing list and found a topic
where the same problem is discussed:[Freesurfer] FreeSurfer 5.2
TRACULA and FSL 5. I've already checked for the things that were
suggested here, but I didn't find a solution. Hoping for some help?
Thanks,
Regards,
Robby
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