Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30098 discussions

surface-based spatial smoothing model
by Francesca Strappini 04 May '16

04 May '16

Hi all, I would like to know which model has been implemented for the surface-based spatial smoothing in Freesurfer (for example in mri_vol2surf). Heat kernel smoothing and/or diffusion smoothing? Thank you Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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downsample fsaverage5 - after and during recon-all
by Wolfers, T. (Thomas) 04 May '16

04 May '16

Is there an easy option to re-sample surface (area.pial and thickness) into fsaverage5 space? How is it possible to use fsaverage5 instead of fsaverage for recon-all? Many thanks for your answers Thomas Wolfers Donders Center for Cognitive Neuroimaging Kapittelweg 29 6525EN Nijmegen The Netherlands Tel: 0031/2436/10098

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Brainstem segmentation
by Haque, Muhammad E 04 May '16

04 May '16

Dear FreeSurfer Users, I would like to know if we can do brainstem segmentation as described in the recent publication http://www.sciencedirect.com/science/article/pii/S1053811915001895 Author as well as FreeSurfer website mention that this feature is only available in FreeSurfer 6.0 and later version https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Where I can download this FreeSurfer 6.0? Thanks. Haque

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Joining the left and the right cortical surface
by Vikash Gupta 03 May '16

03 May '16

Hey everyone, I was wondering, if there is a module in free surfer to join the left and the right cortical surfaces, i.e. the lh.pial and the rh.pial files. I would like to have a contiguous genus 0 cortical brain surface. Any help would be really appreciated. Thans Vikash

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Geodesic distance across hemispheres
by Seung-Goo KIM 03 May '16

03 May '16

Dear freesurfer people, I haven’t noticed that computing geodesic distance between two points across hemispheres is not a trivial as I thought. There are many implementations of Dijkstra algorithm publicly available to compute geodesic distance on a triangular mesh, but it’s a bit tricky to deal with the separated hemispheres. An easy solution could be connecting two meshes: for each medial wall vertex, find a closest (in Euclidian distance) vertex on the medial wall of the other hemisphere, and add a new edge. This would change mesh topology, but it’d be still fine for computing geodesic distance, wouldn’t it? I wish to learn how other people deals with this problem. Best regards, -- Seung-Goo KIM

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Global and lobar gyrification index
by K. Wagstyl 03 May '16

03 May '16

Hi all, Is there a way to calculate total hemispheric and lobar values of gyrification index? Either through a freesurfer-based command or through calculating the convex hull areas independently? We've thought about averaging local gyrification index for the hemisphere but think that direct calculation is probably more appropriate. Thanks, Konrad

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Cortical Parcellation
by Heidi Foo 02 May '16

02 May '16

Dear FreeSurfer Experts, I am currently trying to run cortical parcellation on my subjects. However, I am getting error messages that the --outdir is unknown. This is the command I ran *mri_annotation2label --s FS_PD002_1.nii --hemi lh --lobesStrict --outdir ./label* Is there a way I can resolve this issue? Thank you so much for your kind attention. Best Regards, Heidi Foo

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import ROI analysis results from Matlab into FreeSurfer
by Domenico Zacà 02 May '16

02 May '16

Dear FS experts, I dumped the average cortical thickness values of 68 ROI using aparcstats2table into a spreadsheet, then generated a set of CT networks measures in matlab for each ROI. Now how can I visualize the results back in FreeSurfer? Thanks Domenico Zacà, PhD MR Lab Research Fellow Center for Mind/Brain Sciences University of Trento, Italy Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3069 Fax: +39-0461-28-3066 Email: domenico.zaca(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri

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Reg: Failed to load MRI
by Jesu Kiran Jk 02 May '16

02 May '16

Dear Freesurfer Experts, I wish to load wm.mgz, brain.mgz volumes with freeview. But it is giving me an error 'Failed to load MRI'. Why is it giving me this error and how could I correct this? Please help. Kind Regards, Jesu

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Command for generating spherical surface
by Muhammad Razib 02 May '16

02 May '16

Hi, I have some (freesurfer generated) pial surfaces, but I don't have the sphere surfaces of these. Is there a command in freesurfer to generate .sphere file from .pial file? --- Muhammad Razib

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