Hi Sky,
what are the first few lines of: /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
is your partition full?
Bruce
On Wed, 16 Apr 2008, 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-In tercept-thickness.mat --C/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Diff-v 3-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-In tercept-thickness.mat --C/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Diff-v 3-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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
what are the last couple of lines of that file? On Thu, 17 Apr 2008, Sky Raptentsetsang wrote:
Hi Nick,
When I try to load the lh.cortex.label in tksurfer I get the following error print out in the SSh tool window:
[sky@sosf 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 ($session) set to: surfer: /cind/00/FSv4Test/Freesurfer/subjects surfer: Reading header info from /cind/00/FSv4Test/Freesurfer/subjects/average/mri/T1.mgz reading group avg surface area 1079 cm^2 from file Reading in average area /cind/00/FSv4Test/Freesurfer/subjects/average/surf/lh.pial.avg.area.mgh surfer: vertices=163842, faces=327680 Loading /opt/freesurfer4.0.2/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /opt/freesurfer4.0.2/lib/tcl/tksurfer.tcl Reading /opt/freesurfer4.0.2/lib/tcl/tkm_common.tcl Reading /opt/freesurfer4.0.2/lib/tcl/tkm_wrappers.tcl Reading /opt/freesurfer4.0.2/lib/tcl/fsgdfPlot.tcl Reading /opt/freesurfer4.0.2/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % tksurfer.bin: could not parse 149955th line in /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label
At 07:59 PM 4/16/2008, Nick Schmansky wrote: Sky,
Can you load the lh.cortex.label file in tksurfer? If not, then its corrupted somehow, and would need to be recreated outside of qdec. Nick On Wed, 2008-04-16 at 17:49 -0700, Sky Raptentsetsang wrote: > Hello Freesurfers, > > I am having troubles analyzing some data in the qdec tool. I have two > groups of the same subjects that were run with different versions of > FS and I have put them in the same SUBJECTS_DIR and smoothed and > created an average subject. I have made a qdec.table.dat file and the > appropriate .levels files. The qdec.table.dat file seems to load okay > but once I try to run an analysis i get the attached error messages. > Any ideas on where this error is coming from? It is stating that the > error is coming from a line in text that I don't think exists. > (I have also included the qdec.table.dat) > > erorr.log: > mri_glmfit: could not parse 149955th line > in /cind/00/FSv4Test/Freesurfer/subjects/average/label/lh.cortex.label > > Command print out: > [sky@polaris subjects]$ 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-In tercept-thickness.mat --C/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Diff-v 3-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-In tercept-thickness.mat --C/cind/00/FSv4Test/Freesurfer/subjects/qdec/lh.thickness.version/contrasts/Diff-v 3-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/freesurferSky 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@nmr.mgh.harvard.edu
-
Bruce Fischl -
Nick Schmansky -
Sky Raptentsetsang