Hi Ines
sorry, this was my mistake. The command is "mris_anatomical_stats" NOT "mris_anatomical_thickness". If your SUBJECTS_DIR is set properly, you can run:
mris_anatomical_stats -l $SUBJECTS_DIR/$subject/label/$hemi.cortex \ $subject $hemi
where $hemi is lh or rh and $subject is the subject id you want to quantify
cheers Bruce
On Mon, 12 Aug 2013, Mürner-Lavanchy, Ines wrote:
From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, 9 August 2013 3:36 PM To: Mürner-Lavanchy, Ines Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mean thickness over hemisphere in stats file
Hi Ines
I think mris_anatomical_thickness is your best bet. You probably want to specify the ?h.cortex.label file with the -l flag so that it ignores non-cortical regions
cheers Bruce
On Fri, 9 Aug 2013, Mürner-Lavanchy, Ines wrote:
Dear experts,
please excuse my question, I'm a beginner. I really searched for an answer in the archive, but I couldn't find out what I was doing wrong.
I would like to write the mean cortical thickness of a hemisphere in the stats file. I read one can do that by using -m thickness. Where in the command line do I have to put it? I tried various versions, but it doesn't work.
This would be the command:
aparcstats2table --hemi rh --parc aparc --meas thickness --tablefile "directory"//"filename" --m thickness --subjects 1 2 3 4 SUBJECTS_DIR : "directory"
Where do I include the -m thickness option? Or do I have to add something else?
Thank you very much for your help, Ines
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