---------- Forwarded message ---------- Date: Sat, 18 Jul 2009 13:44:22 +0200 From: Rosa Steimke rosasteimke@gmx.de To: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: writing thickness of ROI to tabel
Hi freesurfer experts, iam trying to get the thichness of a Roi i specified in qdec into a table. i used the mris_anatmical stats command to generate stats for this roi for all participants. I tried the aparc2tabel command with different flags, but the roi i specified was never inside the table. wish flag do i have to use to get the roi that i drew in qdec? thanks in advance! rosa -------- Original-Nachricht --------
Datum: Fri, 17 Jul 2009 14:35:55 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Rosa Steimke rosasteimke@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mris_anatomical_stats
why is there a \ in your command line? On Fri, 17 Jul 2009, Rosa Steimke wrote:
Hi freesurfer experts, I have a problem using the mris_anatomical_stats command to generate
stats for a region of interest that i drew in qdec.
It gives me the following error:
[admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l
rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh
limiting computations to label rh.FUSIFORM.label.
Flagged-options must go first in argument list.
usage: mris_anatomical_stats [options] <subject name> <hemi> [<surface
name>]
This program measures a variety of anatomical properties.
Valid options are:
-i <low thresh> <hi thresh> - only consider thicknesses in the specified range -l <.label file> - limit calculations to specified label -t <thickness file> - use specified file for computing thickness statistics -a <.annot file> - compute properties for each label in the annotation file separately -b - tabular output -f <tablefile> - table output to a file named tablefile (different format than -b) must specify an annotation file with -a or label file with -l -log <log> - will write the stats into a file named <log> -nsmooth <#> - will smooth the thicknessmap # of iterations before using it -c <.ctab file> - output the colortable for this annotation [admins-imac:~/Rosa_MRTs] steimke% mris_anatomical_stats -l
rh.FUSIFORM.label \ -t rh.thickness -b -f 1/stats/rh.FUSIFORM.label 1 rh
do you know what i did wrong? thanks in advance! rosa
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Bruce Fischl