[Freesurfer] mri_watershed

hi, Under freesurfer, how can I force mri_watershed to create 5012 triangles (ico 4) instead of 20480? cheers nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mathematica and freesurfer

Hi, Does anybody have (or know of) functions for reading freesurfer's surface or curvature into Mathematica? Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] color of faces of freesurfer's surfaces

Hi, I can read (in Matlab) the freesurfer's coordinates of vertices but can not find how the colors are defined (i.e. colors of sulci versus gyri). Where can I find this information? best Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvar

[Freesurfer] vertex neighbourhood

hi surfers, Imagine that I need to know what are the closest N vertices (let's say n=100) to a given vertex (i mean two dimentionsal neighourhood on surfaces) . Any idea how to do that? anybody has a written code for this? cheers nima ___ Frees

[Freesurfer] midline errors in pial and white matter boundary

versions? ps. is there any way to add control points for pial surface? cheers nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mgh2 stc

Hi Does anybody have a code to convert mgh format to stc? best Nima Nima Dehghani MD. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] missing curvatures

what is the prob?!?!? any idea? cheers nimA FOR LEFT HEMISPHERE "INFLATED": " env tksurferinterface=csurf patchname= /space/lyon/1/home/inverse/freesurfer_alpha/bin/Linux/tksurfer -sleep_s2 lh inflated -tcl /tmp/TmpTclSurf.12210 MRISreadVertexPositions(/space/humpback/2/users/nima/csur

[Freesurfer] question(s) about brain volume calculation

freesurfer has calculating the surface of the hippocampus. Thanks for your help. -Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only

[Freesurfer] Inquiry About Longitudinal Analysis Using recon-all-clinical.sh

for your time and support! Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you

[Freesurfer] Inquiry About Longitudinal Analysis Using recon-all-clinical.sh

for your time and support! Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you

[Freesurfer] Issue with Voxel Size Mismatch in Samseg-Long Pipeline

ware of in a longitudinal analysis? If there is a better way to handle this issue, I would greatly appreciate your guidance. Best regards, Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

[Freesurfer] Identical values for different cingulate regions

Dear FreeSurfer developers and community, I was reviewing the stats outputs of recon-all from multiple cases processed using FreeSurfer version 6.0.0, and I encountered an unusual issue. Unfortunately, I do not have access to the stats files, but based on the results provided in excel, I have n

Re: [Freesurfer] Issue with Right Hemisphere Segmentation/Parcellation

Thanks for your guidance. I already tried recon-all-clinical.sh; however, I was wondering why did this happen? Could it be related to resampling process or the orientation? Thanks, Nima From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve

[Freesurfer] Corpus Callosum Missing in SAMSEG Output

guidance or suggestions would be greatly appreciated. Please let me know if additional details or files are needed for context. Thank you for your time and support. Best regards, Nima Taghizadeh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Issue with mri_histo_atlas_segment_fireants Command

ance. Best regards, Nima Taghizadeh Mortezaei, M.D. Radiation Oncology Research Fellow, MGH ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intende

[Freesurfer] Issue with Voxel Size Mismatch in Samseg-Long Pipeline

ware of in a longitudinal analysis? If there is a better way to handle this issue, I would greatly appreciate your guidance. Best regards, Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] Inquiry About Longitudinal Analysis Using recon-all-clinical.sh

I appreciate any guidance or recommendations for my question. From: Taghizadeh Mortezaei, Nima Sent: Tuesday, February 11, 2025 9:45:25 AM To: Freesurfer support list Subject: Inquiry About Longitudinal Analysis Using recon-all-clinical.sh Dear FreeSurfer

[Freesurfer] CSF Volume difference between recon-all-clinical and SAMSEG

for your time and assistance! Best regards, Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is