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 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.obermueller@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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