External Email - Use Caution
If you still have the VM setup on your machine, you
can open a new terminal window and then you should see the Freesurfer
Environment is setup,
FREESURFER_HOME /home/developer/7.2.0/dev
FSFAST_HOME /home/developer/7.2.0/dev/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR
/home/developerfreesurfer/7.2.0/subjects
MNI_DIR
/home/developer/7.2.0/mni
garnet2[0]:tmp$ ls $FREESURFER_HOME/bin/aparc*
The aparc* and aseg* commands should all be in your path, i.e.
$ which aparc_stats_aseg
/home/developer/7.2.0/bin/aparc_stats_aseg
$ which aparcstats2table
/home/developer/7.2.0/bin/aparcstats2table
$ which aparcstatsdiff
/home/developer/7.2.0/bin/aparcstatsdiff
$ which aparc2feat
/home/developer/7.2.0/bin/aparc2feat
$ which aseg2feat
/home/developer/7.2.0//bin/aseg2feat
$ which asegstats2table
/home/developer/7.2.0//bin/asegstats2table
$ which asegstatsdiff
/home/developer/7.2.0//bin/asegstatsdiff
You should be able to get some info about the commands using the "-h" or help
option.
garnet2[0]:tmp$ aparcstats2table -h
Usage:
Converts a cortical stats file created by recon-all and or
mris_anatomical_stats (eg, ?h.aparc.stats) into a table in which
each line is a subject and each column is a parcellation. By
default, the values are the area of the parcellation in mm2. The ...
..... rest of output deleted ....
- R.
On 5/21/24 07:45, Carina Obermüller (carina.obermuel...@live.at) wrote:
External Email - Use Caution
Dear Freesurfer team,
I am looking for a group stats command like the asegstats2table and
aparcstats2table command for hipposubfields, brainstem and amygdalar, but I
couldn’t find it in the archives. I remember it was mentioned in the recent
Freesurfer course, but I can’t find it anymore. Could you help me out?
Also more generally, is there an overview page of all the possible group stats
commands?
Thank you so much in advance for your reply!
Sincerely,
Carina
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