Sky,
Can you load the lh.cortex.label file in tksurfer? If not, then its corrupted somehow, and would need to be recreated outside of qdec.
Nick
On Wed, 2008-04-16 at 17:49 -0700, Sky Raptentsetsang wrote:
Hello Freesurfers,
I am having troubles analyzing some data in the qdec tool. I have two groups of the same subjects that were run with different versions of FS and I have put them in the same SUBJECTS_DIR and smoothed and created an average subject. I have made a qdec.table.dat file and the appropriate .levels files. The qdec.table.dat file seems to load okay but once I try to run an analysis i get the attached error messages. Any ideas on where this error is coming from? It is stating that the error is coming from a line in text that I don't think exists. (I have also included the qdec.table.dat)
erorr.log: mri_glmfit: could not parse 149955th line in /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
Command print out: [sky@polaris subjects]$ qdec & [1] 20069 [sky@polaris subjects]$ Using Freesurfer version 4.
Subjects Directory is /cind/00/FSv4Test/Freesurfer/subjects Sessions Directory is /home/sky/sessions
Reading /opt/freesurfer4.0.2/lib/tcl/tkUtils.tcl Using /opt/freesurfer4.0.2/lib/tcl/fsgdfPlot.tcl
Loading data table /cind/00/FSv4Test/Freesurfer/subjects/qdec.table.dat... Number of columns: 5 fsid column: 1 Number of factors: 4 Number of subjects: 68 . . . . . $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /cind/00/FSv4Test/Freesurfer/subjects cmdline mri_glmfit -- y /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/y.mgh --fsgd /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/qdec.fsgd --glmdir /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version --surf average lh --label /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label --C /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Avg-Intercept-thickness.mat --C /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Diff-v3-v4-Intercept-thickness.mat sysname Linux hostname polaris.v21.med.va.gov machine x86_64 user sky FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/y.mgh logyflag 0 usedti 0 FSGD /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/qdec.fsgd labelmask /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label maskinv 0 glmdir /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version DoFFx 0 Creating output directory /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version Loading y from /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/y.mgh Matrix condition is 1 mri_glmfit: could not parse 149955th line in /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label ERROR reading /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label Error in Analyze: command failed: mri_glmfit -- y /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/y.mgh --fsgd /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/qdec.fsgd --glmdir /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version --surf average lh --label /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label --C /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Avg-Intercept-thickness.mat --C /cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Diff-v3-v4-Intercept-thickness.mat
Thanks in advance.
Sky Raptentsetsang
Staff Research Associate CIND, San Francisco VAMC Department of Radiology, UCSF 4150 Clement St. Bldg. 13, 2nd Floor, Mail Stop 114M San Francisco, CA 94121 Phone 415.221.4810 ext. 4186 Fax 415.386.3954
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