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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: https://secure-web.cisco.com/1T5bJ3eWFAY4iTktVauuA7egh6T999ndbgGMUBtHxahqEZX...) 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:
External Email - Use CautionHi 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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