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.
