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