hi freesurfers,
i am running into a segfault whenever i try to use mri_glmfit to run a random effects analysis. (this is in the volume, not on the surface.)
here's my call:
mri_glmfit \ --y $ces_fpath \ --X $design_mat_fpath \ --C $c1_fpath \ --C $c2_fpath \ --C $c3_fpath \ --mask $mask_fpath \ --glmdir $glmdir_fpath \ --nii.gz
i've tried a number of things to reduce the memory footprint of the call: -- originally i was using WLS, but i was worried about the memory demands of the cesvar, so i switched to OLS -- i introduced a GM mask -- i downsampled the ces and cesvar images (from 1 mm isotropic [cvs space] to 2 mm isotropic)
any thoughts on what could be going wrong here?
thanks, guys!
alex
ps. below are my build stamp, my info dump from mri_glmfit, and an example stderr & stdout.
my fs build stamp: freesurfer-Linux-centos4_x86_64-dev-20120104
the "all info" dump from mri_glmfit: ProgramName: mri_glmfit ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2013/05/07-14:15:28-GMT BuildTimeStamp: Jan 4 2012 05:11:02 CVS: $Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ User: alexkell Machine: ba7 Platform: Linux PlatformVersion: 2.6.38-16-generic CompilerName: GCC CompilerVersion: 30400
an example stderr and stdout:
$Id: mri_glmfit.c,v 1.209 2011/12/16 19:02:28 greve Exp $ cwd /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_output/F-O cmdline mri_glmfit --y /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz --wls /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz --X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//asd.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc.mtx --C /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//tc-asd.mtx --mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz --glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O --yhat-save --eres-save --save-cond --nii.gz sysname Linux hostname ba7 machine x86_64 user alexkell FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz logyflag 0 X /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//design_matrix.dat usedti 0 mask /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input/cvs.gmMask.2x2x2.nii.gz maskinv 0 glmdir /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_input//cvs.all.cesvar.F-O.runs_1234.2x2x2.nii.gz weightinv 1 weightsqrt 1 Creating output directory /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O Loading y from /mindhive/nklab2/ellison_on_nklab2/adultasd/vss/4_rfx/glm_input/cvs.all.ces.F-O.runs_1234.2x2x2.nii.gz Saving design matrix to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/Xg.dat Normalized matrix condition is 1 Matrix condition is 2.21429 Pruning voxels by thr: 0.000000 Found 115353 voxels in mask Saving mask to /mindhive/nklab/projects/ellison/adultasd/vss/4_rfx/glm_output//F-O/mask.nii.gz search space = 922824.000000 Segmentation fault