segfault during rfx with mri_glmfit - Freesurfer

7 May 2013


      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