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Hi Renxi,

Because there is typically a bit of error when you do the MNI152-native projection, you should use the Choi parcellation with the "loose mask" (see snapshots here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/StriatumParcellation_Choi2012) and project it from MNI152 to the individual subject's native subject space.

After that you can use the freesurfer anatomical segmentation of putamen + caudate + nucleus accumbens (I hope my memory is correct!) in subject's native space to mask the projected Choi's parcellation.

Regards,
Thomas

On Sun, Nov 15, 2020 at 4:16 PM RENXI LI <rli296@wisc.edu> wrote:
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Hi Freesurfer Experts:

In $FREESURFER_HOME/average/Choi_JNeurophysiol12_MNI152 directory, there are a striatum parcellation masks based on functional connectivities to the cortical networks by Yeo et al 2011. I would like to register this striatum parcellation mask to each subject’s striatum mask. But to create the striatum mask in the native subject space using mri_binarize, which segmentation file do you recommend to use and which segmentations should I be including in the mask to cover all regions in Choi’s striatum mask?

Best,
Renxi

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