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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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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ut_CRqJ3rxIZhF_3G5uoABokb2Lwfbv79ge0a455HMmUzG...
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Hi Dr. Yeo:
Thank you! That is very helpful!
Best, Renxi
On Nov 16, 2020, at 6:58 PM, Thomas Yeo <ythomas@csail.mit.edumailto:ythomas@csail.mit.edu> wrote:
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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://secure-web.cisco.com/1ow8rGywnkjIE0IIWJRhBTPcZ_1mUrILhbE9oKuiPUUzAtV...https://secure-web.cisco.com/1T5bJ3eWFAY4iTktVauuA7egh6T999ndbgGMUBtHxahqEZXNLw8GIN83oTyKPzaNSqGnCYXwUBRiti3k4KWBDM2yjjREJmM5upv_2JKSG9MoKW6D8fSPmmhWK1jcdPYjk7phjBySaiL2Mkmqy9KQKD8zWY1v5J3A8dS3soDuIacpuCj7ZOw3WfliM6uBBcD0D1Xi0k-Px-VWTZ2WGhoB9d8FZgqsx-NvHR2-RYtlry__PgpyVkB9A5FtjllHSxTmevoEAI0_vBEtQ-q0vT-lacw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FStriatumParcellation_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.edumailto:rli296@wisc.edu> wrote: External Email - Use Caution
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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/19qkHfvAm9IU4BctdrbqClPO7fOOTDc_YOjOrip-xBkPQCT...https://secure-web.cisco.com/1ut_CRqJ3rxIZhF_3G5uoABokb2Lwfbv79ge0a455HMmUzGUcNQhdd52spSm4QZvkG7_zJ_xf_tAl9nocUyOCAsLcLdmIHU9lA_foWZAMGWFxUyhnnkviKL3nsTPyG25CI69iIS4DaW37fOD5ZRW-V7tDSddVIehWgQC0bLN2cNCnNw1H9VZ3fNKRUx4oJwDZiiH0tAlRNiD4VUu1CYJTrjCFfxOqwRGh-W_amGV-vtPwjsDE7culLaq6nvC2fYeHcHqHiIsO7QQywfe721eLIg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/19qkHfvAm9IU4BctdrbqClPO7fOOTDc_YOjOrip-xBkPQCT...
freesurfer@nmr.mgh.harvard.edu
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RENXI LI -
Thomas Yeo