When I try to load the lh.cortex.label in tksurfer I get the following error print out in the SSh tool window:
[EMAIL PROTECTED] subjects]$ tksurfer average lh pial
Using Freesurfer version 4.
Subjects Directory is /cind/00/FSv4Test/Freesurfer/subjects
Sessions Directory is /home/sky/sessions
surfer: current subjects dir: /cind/00/FSv4Test/Freesurfer/subjects
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /cind/00/FSv4Test/Freesurfer/subjects
surfer: Reading header info from /cind/00/FSv4Test/Freesurfer/subjects/average/mri/T1.mgz
reading group avg surface area 1079 cm^2 from file
Reading in average area /cind/00/FSv4Test/Freesurfer/subjects/average/surf/lh.pial.avg.area.mgh
surfer: vertices=163842, faces=327680
Loading /opt/freesurfer4.0.2/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: using interface /opt/freesurfer4.0.2/lib/tcl/tksurfer.tcl
Reading /opt/freesurfer4.0.2/lib/tcl/tkm_common.tcl
Reading /opt/freesurfer4.0.2/lib/tcl/tkm_wrappers.tcl
Reading /opt/freesurfer4.0.2/lib/tcl/fsgdfPlot.tcl
Reading /opt/freesurfer4.0.2/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
% tksurfer.bin: could not parse 149955th line in /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
At 07:59 PM 4/16/2008, Nick Schmansky wrote:
Sky,
Can you load the lh.cortex.label file in tksurfer? If not, then its
corrupted somehow, and would need to be recreated outside of qdec.
Nick
On Wed, 2008-04-16 at 17:49 -0700, Sky Raptentsetsang wrote:
> Hello Freesurfers,
>
> I am having troubles analyzing some data in the qdec tool. I have two
> groups of the same subjects that were run with different versions of
> FS and I have put them in the same SUBJECTS_DIR and smoothed and
> created an average subject. I have made a qdec.table.dat file and the
> appropriate .levels files. The qdec.table.dat file seems to load okay
> but once I try to run an analysis i get the attached error messages.
> Any ideas on where this error is coming from? It is stating that the
> error is coming from a line in text that I don't think exists.
> (I have also included the qdec.table.dat)
>
> erorr.log:
> mri_glmfit: could not parse 149955th line
> in /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
>
> Command print out:
> [EMAIL PROTECTED] subjects]$ 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
> [email protected]
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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