Cerebellum extraction

AFNI Message Board
1

Hello AFNI

I want to extract the cerebellum of the subrick 4 “GC_mask” of the MNI152_2009_template_SSW.nii. Would you mind to guide me how to do it?

Thank you

2

You could use the Jorn Diedrichsen’s SUIT cerebellum atlas as an additional mask. We have an older version here that seems to make the MNI 2009c template well. There are two versions of the atlases - one for the MNI space (useful here) and another when aligning to the SUIT cerebellum template specifically.

https://afni.nimh.nih.gov/pub/dist/atlases/SUIT_Cerebellum/SUIT_2.6_1/

Alternatively, get a newer version here. The site requires registration before you can download. I haven’t gone through the atlas and masks in detail myself though, but they appear roughly right. Some are a little too big or a little too small. Take a look and see if those will work for your needs.
http://www.diedrichsenlab.org/imaging/suit_download.htm

For the one from the AFNI site, you could do something like this to combine the masks:


3dcalc -a MNI152_2009_template_SSW.nii.gz'[4]' -b Cerebellum-MNIsegment.nii.gz -expr 'a*step(b)' \
  -prefix MNI_GC_cerebellum.nii.gz

You can also use the FreeSurfer segmentation for the MNI 2009c template here:
https://afni.nimh.nih.gov/pub/dist/tgz/suma_MNI152_2009.tgz

The cerebellum regions are just about 4 regions (not including brainstem or fourth ventricle), and you can combine those with the GC mask from the template.


3dcalc - a MNI152_2009_template_SSW.nii.gz'[4]' \
    -b aparc+aseg_REN_all.nii.gz'<Left-Cerebellum-Cortex,Right-Cerebellum-Cortex,Left-Cerebellum-White-Matter,Right-Cerebellum-White-Matter>' \
    -expr 'a*step(b)' -prefix MNI_GC_FScerebellum.nii.gz
3

Thank you so much Daniel, that was super helpful!

Have a nice day :slight_smile: