Hi Yuko, I think you must have an older version of glmfit-sim some how. I've put a newer version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim-v5.0 copy this to your $FREESURFER_HOME/bin/mri_glmfit-sim (ie, change the name; and make a backup copy). doug
yukoyy wrote: > 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 > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
