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
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
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
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
Yes, of course. Here I send it. Best regards, Fernando ________________________________________ From: Anastasia Yendiki [ayendiki@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
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
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.
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
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 [ayendiki@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
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
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.
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
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Fernando Ventrice