Dear freesurfer users
I got an error message during mri_glmfit. (please see below my error message) I was able to find 'mri_glmfit.log' file in './glm/lh.dx_age.glmdir' directory
Thank you for advance --------------------------------------------------- These are my constrasts. : to construct the contrast vector for testing volume change according to age = age.mat 0 0 0 1 : for effect of interest (ANOVA: f test) -> Am I right? 1 0 0 0 0 1 0 0 0 0 1 0 : for difference btw 3 group independent of age -> Am I right? -1 0 1 0 0 -1 1 0
There are three class and one variable (see below my FSGD file) # FSGD file GroupDescriptorFile 1 Title Thickness vs Dx and Age Class A circle blue Class B circle green Class C plus red Variables Age Input 61 A 71 Input 54 A 72 Input 12 B 74 Input 33 B 77 Input 63 C 80 Input 01 C 87 ...... DefaultVariable Age
# Error message mri_glmfit --y lh.dx_age.thickness.10.mgh --fsgd my_dx_age_1_fsgd.txt doss --glmdir lh.dx_age.glmdir --surf average lh --C age.mat gdfReadHeader: reading my_dx_age_1_fsgd.txt INFO: ignoring tag vs INFO: gd2mtx_method is doss Reading source surface /GR/average/surf/lh.white reading group avg surface area 936 cm^2 from file Reading in average area /GR/average/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 62167.195312 AvgVtxArea 0.379434 AvgVtxDist 0.717000 StdVtxDist 0.244431
$Id: mri_glmfit.c,v 1.83 2006/03/10 23:26:51 greve Exp $ cwd /GR/group_analysis/glm cmdline mri_glmfit --y lh.dx_age.thickness.10.mgh --fsgd my_dx_age_1_fsgd.txt doss --glmdir lh.dx_age.glmdir --surf average lh --C age.mat sysname Linux hostname *** machine x86_64 user *** FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /GR/group_analysis/glm/lh.dx_age.thickness.10.mgh FSGD my_dx_age_1_fsgd.txt glmdir lh.dx_age.glmdir Creating output directory lh.dx_age.glmdir Loading y from /GR/group_analysis/glm/lh.dx_age.thickness.10.mgh Matrix condition is 177.843 search space = 93594.7 Segmentation fault
I can't figure out what's happening, so I'll probably need the data. Can you tar up the input data, the fsgd, and the contrast matrices and drop them for me at: www.nmr.mgh.harvard.edu/facility/filedrop?
Bum Seok Jeong wrote:
Dear freesurfer users
I got an error message during mri_glmfit. (please see below my error message) I was able to find 'mri_glmfit.log' file in './glm/lh.dx_age.glmdir' directory
Thank you for advance
These are my constrasts. : to construct the contrast vector for testing volume change according to age = age.mat 0 0 0 1 : for effect of interest (ANOVA: f test) -> Am I right? 1 0 0 0 0 1 0 0 0 0 1 0 : for difference btw 3 group independent of age -> Am I right? -1 0 1 0 0 -1 1 0
There are three class and one variable (see below my FSGD file) # FSGD file GroupDescriptorFile 1 Title Thickness vs Dx and Age Class A circle blue Class B circle green Class C plus red Variables Age Input 61 A 71 Input 54 A 72 Input 12 B 74 Input 33 B 77 Input 63 C 80 Input 01 C 87 ...... DefaultVariable Age
# Error message mri_glmfit --y lh.dx_age.thickness.10.mgh --fsgd my_dx_age_1_fsgd.txt doss --glmdir lh.dx_age.glmdir --surf average lh --C age.mat gdfReadHeader: reading my_dx_age_1_fsgd.txt INFO: ignoring tag vs INFO: gd2mtx_method is doss Reading source surface /GR/average/surf/lh.white reading group avg surface area 936 cm^2 from file Reading in average area /GR/average/surf/lh.white.avg.area.mgh Number of vertices 163842 Number of faces 327680 Total area 62167.195312 AvgVtxArea 0.379434 AvgVtxDist 0.717000 StdVtxDist 0.244431
$Id: mri_glmfit.c,v 1.83 2006/03/10 23:26:51 greve Exp $ cwd /GR/group_analysis/glm cmdline mri_glmfit --y lh.dx_age.thickness.10.mgh --fsgd my_dx_age_1_fsgd.txt doss --glmdir lh.dx_age.glmdir --surf average lh --C age.mat sysname Linux hostname *** machine x86_64 user *** FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /GR/group_analysis/glm/lh.dx_age.thickness.10.mgh FSGD my_dx_age_1_fsgd.txt glmdir lh.dx_age.glmdir Creating output directory lh.dx_age.glmdir Loading y from /GR/group_analysis/glm/lh.dx_age.thickness.10.mgh Matrix condition is 177.843 search space = 93594.7 Segmentation fault _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bum Seok Jeong -
Doug Greve