Many thanks, yes, it did work well.
But, than I ran "freeview
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5
-viewport 3d"
and got the following message:
bash-3.2$ freeview
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5
-viewport 3d2015-09-29 00:23:47.366 Freeview[22019:303] invalid
drawable2015-09-29 00:23:47.367 Freeview[22019:303] invalid drawable2015-09-29
00:23:47.385 Freeview[22019:303] invalid drawable2015-09-29 00:23:47.386
Freeview[22019:303] invalid drawable2015-09-29 00:23:47.399 Freeview[22019:303]
invalid drawable2015-09-29 00:23:47.400 Freeview[22019:303] invalid
drawable2015-09-29 00:23:47.420 Freeview[22019:303] invalid drawable2015-09-29
00:23:47.421 Freeview[22019:303] invalid drawable
Unrecognized sub-option flag 'annot=aparc.annot'.
Freeview has opened, but it showed no results at all:-(
What should I do? I read that one has to upgrade the newest freeview-version?
Is it possible to get the newest version without installing freesurfer again?
Many thanks!
Dusan
Date: Mon, 28 Sep 2015 11:35:50 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] 3_group_comparison
Did you include the back slashes in your command? If so, remove them
and retry.
On 9/25/15 7:11 PM, Dusan Hirjak wrote:
Dear Freesurfer experts,
I am trying to compare 3 groups (aut, sch,
ges) according to thickness, area and LGI at once (omnibus
test).
I did run the following command:
mris_preproc
--fsgd NSS_3_GR.fsgd \ --cache-in
thickness.fwhm15.fsaverage \ --target fsaverage --hemi lh
\ --out lh.NSS_3_GR.thickness.15.mgh
This step did
work properly:-)
Now, Im trying
to run the following command, but it does not work:
mri_glmfit \ --y
lh.NSS_3_GR.thickness.15.mgh \ --fsgd NSS_3_GR.fsgd dods\
--C contrasts.mtx \ --surf fsaverage lh \ --cortex \
--glmdir NSS_3_GR.glmdir
I got this
message: "ERROR:
Option --y unknown"
What am I doing
wrong?
Thank you for
your help!
Best regards
Dusan
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