External Email - Use Caution
Hi FS experts,
We are running the segmentHA_T2.sh script, and we get the .mgz files for the 3 hierarchies (CA, FS60, and HBT), but when we run either concatenatesubregions or asegstats2table, we get the fine grain hippocampal subfield volumes. Is it possible to extract the volumes (as .txt) from the hierarchy .mgz files? We are interested in using the CA hierarchy, and we are not sure how to calculate this with the output we receive from either concatenatesubregions/asegstats2table.
Any help is appreciated! Erin
Dear Erin, I would recommend taking the spreadsheet with the fine-grained volumes, and simply combine the volumes (columns) as follows: CA1 = CA1-head + CA1-body CA3 = CA3-head + CA3-body CA4 = CA4-head + CA4-body GC-ML-DG = GC-ML-DG -head + GC-ML-DG -body Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Erin L Ratliff eratlif2@umd.edu Date: Thursday, March 13, 2025 at 11:16 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal Subfield Hierarchies
External Email - Use Caution Hi FS experts,
We are running the segmentHA_T2.sh script, and we get the .mgz files for the 3 hierarchies (CA, FS60, and HBT), but when we run either concatenatesubregions or asegstats2table, we get the fine grain hippocampal subfield volumes. Is it possible to extract the volumes (as .txt) from the hierarchy .mgz files? We are interested in using the CA hierarchy, and we are not sure how to calculate this with the output we receive from either concatenatesubregions/asegstats2table.
Any help is appreciated! Erin
External Email - Use Caution
Thank you for your reply, Eugenio!
How do we get values described here: "Molecular subregion added to nearest neighbor: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields. GC-ML-DG is absorbed by CA4, and the voxels in the molecular layer are assigned the label of the closest voxel that is neither molecular layer nor background (suffix: "CA")." Is it possible to get this information by extracting the volumes from the CA hierarchy mgz files?
Thank you! Erin
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Date: Friday, March 14, 2025 at 5:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfield Hierarchies Dear Erin, I would recommend taking the spreadsheet with the fine-grained volumes, and simply combine the volumes (columns) as follows: CA1 = CA1-head + CA1-body CA3 = CA3-head + CA3-body CA4 = CA4-head + CA4-body GC-ML-DG = GC-ML-DG -head + GC-ML-DG -body Cheers, /Eugenio -- Juan Eugenio Iglesias http://secure-web.cisco.com/1gXmO0EbMO44I3mvGyNReTfeVYX-nGiwGOAd38sDXqrJ1bJL...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Erin L Ratliff eratlif2@umd.edu Date: Thursday, March 13, 2025 at 11:16 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal Subfield Hierarchies
External Email - Use Caution Hi FS experts,
We are running the segmentHA_T2.sh script, and we get the .mgz files for the 3 hierarchies (CA, FS60, and HBT), but when we run either concatenatesubregions or asegstats2table, we get the fine grain hippocampal subfield volumes. Is it possible to extract the volumes (as .txt) from the hierarchy .mgz files? We are interested in using the CA hierarchy, and we are not sure how to calculate this with the output we receive from either concatenatesubregions/asegstats2table.
Any help is appreciated! Erin
It can be done but only with the “hard” (discrete) segmentations, i.e., by counting voxels yourself (and multiplying by the voxel size in cubic mm, which is 1/27!) Cheers, /Eugenio
-- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Erin L Ratliff eratlif2@umd.edu Date: Monday, March 17, 2025 at 10:12 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfield Hierarchies
External Email - Use Caution Thank you for your reply, Eugenio!
How do we get values described here: "Molecular subregion added to nearest neighbor: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields. GC-ML-DG is absorbed by CA4, and the voxels in the molecular layer are assigned the label of the closest voxel that is neither molecular layer nor background (suffix: "CA")." Is it possible to get this information by extracting the volumes from the CA hierarchy mgz files?
Thank you! Erin
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. JIGLESIASGONZALEZ@mgh.harvard.edu Date: Friday, March 14, 2025 at 5:44 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfield Hierarchies Dear Erin, I would recommend taking the spreadsheet with the fine-grained volumes, and simply combine the volumes (columns) as follows: CA1 = CA1-head + CA1-body CA3 = CA3-head + CA3-body CA4 = CA4-head + CA4-body GC-ML-DG = GC-ML-DG -head + GC-ML-DG -body Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Erin L Ratliff eratlif2@umd.edu Date: Thursday, March 13, 2025 at 11:16 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal Subfield Hierarchies
External Email - Use Caution Hi FS experts,
We are running the segmentHA_T2.sh script, and we get the .mgz files for the 3 hierarchies (CA, FS60, and HBT), but when we run either concatenatesubregions or asegstats2table, we get the fine grain hippocampal subfield volumes. Is it possible to extract the volumes (as .txt) from the hierarchy .mgz files? We are interested in using the CA hierarchy, and we are not sure how to calculate this with the output we receive from either concatenatesubregions/asegstats2table.
Any help is appreciated! Erin
freesurfer@nmr.mgh.harvard.edu
-
Erin L Ratliff -
Iglesias Gonzalez, Juan E.