External Email - Use Caution Hi Dr. Yeo:
Thank you! That is very helpful! Best, Renxi On Nov 16, 2020, at 6:58 PM, Thomas Yeo <ytho...@csail.mit.edu<mailto:ytho...@csail.mit.edu>> wrote: External Email - Use Caution 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_1mUrILhbE9oKuiPUUzAtVW-JjIWQHSnpjNtfI3J_xh_0yeRVV4VBaAgA5rG4vjoTZ5f-TCaXtwTetiIsAVbeWnwar5lZcDnoGyqS8saEQav1teely7yTQTej4H1Lhhy7HAxz_csiWxuU1qGv3DcihcN0BeHmdv8EzRj63y3aVwH4sXYWKUJiG2g2HrbqWKi43NqBGXH1L2rCINC-dv6rM5t7bGPEl_eJ6QttGmtmI7x9T9x6caC_YNwiHbjMg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FStriatumParcellation_Choi2012<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 <rli...@wisc.edu<mailto:rli...@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.edu<mailto: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-xBkPQCTln3NvQbpDOjFt19h2UXbVfUymr4cHS47WHNrhANbv8gM1ShoBz_fXHfDMfMjOcpCMvXy9CfZWyqoaO2MlWDbLEM0z9ExH90tme4RjCRiDz39kwC-SqDaUeTSg0S3br4nwFSqR-lt0Otqd9lPbxQ_860lX6BxIDU5tsei2m-EyYmuWFI_cbX8_W-eHOyqi3vBe7eYpjm70pHUDbV1lqmHPjF4XDZQ79HmY0bB7-kQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer<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.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/19qkHfvAm9IU4BctdrbqClPO7fOOTDc_YOjOrip-xBkPQCTln3NvQbpDOjFt19h2UXbVfUymr4cHS47WHNrhANbv8gM1ShoBz_fXHfDMfMjOcpCMvXy9CfZWyqoaO2MlWDbLEM0z9ExH90tme4RjCRiDz39kwC-SqDaUeTSg0S3br4nwFSqR-lt0Otqd9lPbxQ_860lX6BxIDU5tsei2m-EyYmuWFI_cbX8_W-eHOyqi3vBe7eYpjm70pHUDbV1lqmHPjF4XDZQ79HmY0bB7-kQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
