Hello I'm having a trouble with mri_glmfit-sim with v5.0, which is locally installed on Mac 10.6.8.
Whan I ran: mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166 I got: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd I have /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd in my directory. It looks like I need to somehow tell freesurfer "/fsaverage/lh/", but how? Before mri_glmfit-sim, I did the followings: isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh -c 16vs4 -o MPgroup mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz % ------------------------------------------------------------------------- Also, when I did: mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite I got several warnings and errors (full error message pasted at the end of this email): > cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface > fsaverage lh --glmdir MPglm.wls --nii.gz > WARNING: unrecognized mri_glmfit cmd option --surface > WARNING: unrecognized mri_glmfit cmd option fsaverage > WARNING: unrecognized mri_glmfit cmd option lh > WARNING: unrecognized mri_glmfit cmd option --nii.gz .... > mri_glmfit --y > /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii > --C > MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim > mc-z 100 2 MPglm.wls/csd > /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls > /Users/kawabata/Documents/freesurfer > /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii > Bus error I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? When I paste "mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz" in the command line, it works without any error. Thanks in advance! Yuko Yotsumoto % full error message regarding the second question ------------------------------------------- cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz WARNING: unrecognized mri_glmfit cmd option --surface WARNING: unrecognized mri_glmfit cmd option fsaverage WARNING: unrecognized mri_glmfit cmd option lh WARNING: unrecognized mri_glmfit cmd option --nii.gz log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log cd /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4 /Applications/freesurfer/bin/mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite $Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $ Wed Nov 23 13:55:01 JST 2011 Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 kawabata setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 15.248189 nSimPerJob = 100 1/1 Wed Nov 23 13:55:01 JST 2011 mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd/mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii Bus error _______________________________________________ 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.
