hi doug,

thanks for the quick response.  

i got it to work -- apparently the 5.1.x developmental version i was using had some problem in mri_glmfit.  when i switched to the stable 5.1 version (build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0) it ran perfectly smoothly.  

unfortunately, i'm not sure how useful it would be to others on this listserv. :-)


alex



On Tue, May 7, 2013 at 2:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
Hi Alex, is it actually running out of memory? Otherwise, nothing comes
to mind. If you tar up all the inputs and drop them at our file drop
I'll take a look.
doug


On 05/07/2013 10:24 AM, Alex Kell wrote:
> 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
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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