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 [fis...@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
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.
_______________________________________________
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.
