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 <gr...@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 > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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