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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