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: > [EMAIL PROTECTED] subjects]$ qdec & > [1] 20069 > [EMAIL PROTECTED] 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
