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: https://secure-web.cisco.com/1RCrRYR2kfqIYN7pxC6sGgF_XvdqzAAephS3DadIADfMm-6...) 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
External Email - Use Caution
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-bounces@nmr.mgh.harvard.edu on behalf of "Boa Sorte Silva, Narlon" narlon.silva@ubc.ca Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, November 27, 2023 at 4:20 PM To: freesurfer 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/1JmbBV86Tak0d8hlYwX2j2lbFduvB1TXb8SuiSz1dCoDi3w...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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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 glasserm@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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Boa Sorte Silva, Narlon" <narlon.silva@ubc.ca mailto:narlon.silva@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/1LYOtQ5QZM01untBuVB2rnBzizOAUXkcpb4Bxazx83j2cJN... 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1cXMzcDcOGeD3A8Xd1SZ5FkSXZkKULAlG9pgR6cwvDcSK5l... Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Boa Sorte Silva, Narlon -
Glasser, Matt