Hi Fernando - You need to provide you bvecs and bvals files explicitly in
your configuration file. The first error occurs b/c these files are
missing.
a.y
On Thu, 11 Oct 2012, Fernando Ventrice wrote:
Yes, of course. Here I send it. Best regards,
Fernando
________________________________________
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Thursday, October 11, 2012 1:50 PM
To: Fernando Ventrice
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] TRACULA trac-all -path ERROR
Hi Fernando - Can you please send your scripts/trac-all.log file? My guess
is something went wrong earlier in the process that caused those files not
to be created.
Thanks,
a.y
On Thu, 11 Oct 2012, Fernando Ventrice wrote:
Dear Freesurfer-Tracula users,
I'm trying to use Tracula to analyze some DTI images. I already used Freesurfer
and FSL without problems. First of all, my system is the following:
Linux Xubuntu 12.04 LTS x86_64 - Intel i7 - 8Gb RAM - Nvidia GeForce GT 520 1GB
Freesurfer version 5.1.0
(freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz)
FSL version 5.0.1 (from Neurodebian)
The first problem I had was with the first command: "trac-all -prep -c dmrirc_file" gave
an error about not finding the 'job' command. This was solved (thanks to Anastasia Yendiki) using:
"set runlist=(1)" in the 'dmrirc_file'.
Then, I had some problems with the second command: "trac-all -bedp -c
dmrirc_file", which gave this error:
Queuing preprocessing stages
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE:
unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE:
unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [:
xbedpostx_pre: unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x:
unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le:
argument expected
Queuing parallel processing stage
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE:
unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [:
xbedpostx: unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x43:
unexpected operator
0 slices processed
Queuing post processing stage
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 216: [: NONE:
unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 263: [: NONE:
unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 321: [:
xbedpostx_post: unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 458: [: x:
unexpected operator
/home/labneuroimg/Programs/freesurfer_510/bin/fsl_sub_seychelles: 472: [: -le:
argument expected
Reading about this on the freesurfer mailing-list I got to the conclusion of
running directly:
bedpostx /home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dmri
(in the middle I learned how to use condor!)
It finished without errors. So I went to the last command: "trac-all -path -c
dmrirc_file" which complained about not finding the following file:
ERROR: Could not open
/home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/diff/lh.cst_AS_avg33_mni_flt_cpts_5.txt
These files were at
"/home/labneuroimg/STATION_FLENI/Tensores/subject/TRACULA/subject/dlabel/mni"...
should I copy them to the diff folder??
I send as attachments the error output from "trac-all -path -c dmrirc_file" and the
"dmrirc_file" I used.
Best regards and thanks a lot!
Fernando Ventrice
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El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
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