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
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
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
yukoyy