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
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
you can also use mri_segstats with the --slabel option (spec ?h.cortex.label) and the thickness as the input
On 08/09/2013 09:36 AM, Bruce Fischl wrote:
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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Mürner-Lavanchy, Ines