that looks okay. What about the last two lines? On Thu, 17 Apr 2008, Sky Raptentsetsang wrote:
Hi Bruce,
Here are the first few lines of the lh.cortex.label:
#label , from subject ?? 149955 ==>/cind/00/FSv4Test/Freesurfer/subjects/average/make_cortex_label.tmp.20230/lh.G_a nd_S_occipital_inferior.label <== 161841 -37.845 -74.578 -13.988 0.000000 161842 -37.786 -74.111 -14.300 0.000000 161843 -37.811 -73.715 -14.628 0.000000 161844 -37.907 -73.352 -14.952 0.000000 161865 -37.824 -71.907 -13.407 0.000000 161867 -37.788 -71.373 -13.692 0.000000 161868 -38.012 -72.139 -13.895 0.000000 161869 -38.155 -72.375 -14.413 0.000000 161870 -38.143 -72.648 -14.845 0.000000 161871 -38.084 -72.975 -15.268 0.000000 ==>/cind/00/FSv4Test/Freesurfer/subjects/average/make_cortex_label.tmp.20230/lh.G_a nd_S_transverse_frontopolar.label <== 146036 -10.156 67.319 -1.698 0.000000 146037 -9.764 67.608 -2.021 0.000000 146038 -9.389 67.908 -2.304 0.000000 146039 -8.876 67.922 -0.865 0.000000 146040 -8.929 68.036 -1.708 0.000000 146041 -9.014 68.059 -2.603 0.000000 146042 -8.649 68.148 -2.940 0.000000 146043 -8.286 68.109 -3.301 0.000000 146044 -7.962 67.947 -3.652 0.000000 146045 -7.753 67.564 -3.208 0.000000
At 06:05 PM 4/16/2008, Bruce Fischl wrote: 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/Dif f-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/Dif f-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 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