Hi Anastasia and FS-community

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

Robby.DePauw@Ugent.be

On 09 Sep 2014, at 18:19, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

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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