Thank you! Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSHR BC/CLEAR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon > On Nov 28, 2023, at 3:59 PM, Glasser, Matt <glass...@wustl.edu> wrote: > > [CAUTION: Non-UBC Email] > External Email - Use Caution > > > Sorry, missed this one before I got the personal invitation to respond. > > I believe this would use a FreeSurfer registration of the group parcellation > to the individual. That is a folding-based registration and one can do > slightly better than that with MSMSulc. One can do much better than that > with MSMAll, which is an areal-feature-based registration. Finally, a direct > areal classifier can do even better, and we are working on a new version of > that that is more shareable. Also, there will likely be improvements to the > various registration methods in the future. Coalson et al., (2018) PNAS has > some comparisons of different approaches currently available. > > Matt. > > From: <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Boa Sorte > Silva, Narlon" <narlon.si...@ubc.ca <mailto:narlon.si...@ubc.ca>> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Monday, November 27, 2023 at 4:20 PM > To: freesurfer <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] FreeSurfer Parcellation Using Glasser's Atlas (HCP-MMP1) > > > Hi there, > > I am hoping to extract cortical thickness and volume data from > FreeSurfer-processed subjects using the HCP-MMP1 atlas (Glasser et al 2016 > Nature). I have found many discussions in the email list but I wasn’t able to > understand whether this procedure can be reliably done using .annot files. > > I have found ?h.HCPMMP1.annot files online (e.g., ggsegGlasser: MailScanner > has detected a possible fraud attempt from "secure-web.cisco.com" claiming to > be > https://secure-web.cisco.com/1LYOtQ5QZM01untBuVB2rnBzizOAUXkcpb4Bxazx83j2cJN8Mnj0kqyEtUCK6-Ufat3ebPgy88VEYBmRseqQA8EdYrXVS8KY5U8U2BSeaMBkU56S5HDUL9EP1F2j4eSVGU-XZ2ZflgLGWL95izkxzR-d31cTAW7-a2_XuxCgIfOlOuZs-7Pz-_aPkFRTVp1vM2FLd9kPF0bDGo_rFO9PEu7Fhmwv5TnnzTBbpZnC1NyNNk3tgyvykYofBLRb32_2OLxmnfklz96SlNQkY19ng46Z1zdpOrpx59oyWPOpVxQBabH7UdlpekI7v8ErpbLO0/https%3A%2F%2Fgithub.com%2Fggseg%2FggsegGlasser%2Ftree%2Fmaster%2Fdata-raw > > <https://secure-web.cisco.com/1RCrRYR2kfqIYN7pxC6sGgF_XvdqzAAephS3DadIADfMm-6hoRd0sxcmdWRwYcGtkA-1gc7ZC9mYwzkPFHM8ycIPc3lYKBliI4MlhpBI0pNP7d6nNXhKmziozV7LPHR6bOmLuljZCo6Elu5DfPrDjcK9sXxOTADtFMn_j7QiamMngwTj6ci-kK7weiVMNm48V-1lppYtYxYIF2o33pH_y3e0U1uQqglVKzEK9L4W50PlIBDYIetkga5KuLV3JZ3qULjZufEAQgsKcBIZ09jnE1GKxMWrAVDgQWUqbas9gFiJnELS_7FBm92O9x6kP22Zn/https%3A%2F%2Fgithub.com%2Fggseg%2FggsegGlasser%2Ftree%2Fmaster%2Fdata-raw>) > in fsaverage space, which I have resampled to the subject’s space using > mri_surf2surf as follows: > > # Apply Glasser’s 2016 HCP-MMIP1.0 atlas > mri_surf2surf \ > --hemi ${hemi} \ > --srcsubject fsaverage \ > --trgsubject ${id} \ > --sval-annot fsaverage/label/${hemi}.HCPMMP1.annot \ > --tval ${SUBJECTS_DIR}/${id}/label/${hemi}.HCPMMP1.annot > > > Then I extracted the stats using this command: > > # Extract Thickness and Volume stats > mris_anatomical_stats \ > -a ${SUBJECTS_DIR}/${id}/label/${hemi}.HCPMMP1.annot \ > -f ${SUBJECTS_DIR}/${id}/stats/${hemi}.HCPMMP1.stats \ > -b ${id} ${hemi} > > My question is whether the output from this procedure can be reliably used as > an accurate version of the HCP-MMP1 parcellated regions in the subject’s > native space OR whether a more involved process is needed to generate the > parcellation. > > Thank you for your help > > Best regards, > Nárlon Cássio > > Nárlon C Boa Sorte Silva PhD (He, Him, His) > CIHR and MSHR BC/CLEAR Postdoctoral Research Fellow > Aging, Mobility, and Cognitive Health Lab > Djavad Mowafaghian Centre for Brain Health > Department of Physical Therapy, Faculty of Medicine > University of British Columbia > Vancouver, Canada > Twitter: @BoaNarlon > > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. 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