Re: [Freesurfer] Syntax Error: trac-all -bedp
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
$SUBJECTS_DIR), but this doesn’t seem to fix the problem.
Thanks for the already given advice,
Regards,
Robby
Robby De Pauw, drs.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent
robby.dep...@ugent.be
On 09 Sep 2014, at 18:19, Anastasia Yendiki
wrote:
>
> Hi Robby - Since you're running it locally and not on a cluster, you can
> just run bedpostx directly:
>
> bedpostx /media/mri/DATAPART11/ROBBY/FREESURFER/T1/INP_080_LISA_V_1/dmri
>
> a.y
>
> On Tue, 9 Sep 2014, Robby De Pauw wrote:
>
>>
>> Dear Anastasia, Barbara & FS-community,
>>
>> The preprocessing step of Tracula was succesfully completed. However
>> when I try to do the next step: fitting the Ball & Stick model I get
>> another error:
>>
>> mri@ge24c165:/media/mri/DATAPART11/ROBBY/FREESURFER$ 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
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>
>
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Re: [Freesurfer] Syntax Error: trac-all -bedp
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
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
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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
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[Freesurfer] Syntax Error: trac-all -bedp
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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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.
