Freesurfer May 2016

freesurfer@nmr.mgh.harvard.edu

135 participants
197 discussions

Beyond thickness and local gyration indexes
by Caverzasi, Eduardo 04 May '16

04 May '16

Hi, I am processing data with freesurfer to look at thickness and local gyration index. I noticed that the aparcstats2table allows obtaining other values about curvature index, folding index and mean curvature. We are interested in understanding the folding pattern in children. I am not sure what the latter indexes are referring to precisely and if there is any other metrics we should consider. Best regards, Eduardo

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error in fast_selxavg3 (line 1248)
by S.V.Shepherd [work] 04 May '16

04 May '16

I've modified an analysis to include a vector of noise time courses estimated using ICA. Since IC effects should be consistent across runs, I'm using taskregs instead of nuisregs. I can define the analysis and set up contrasts fine; however, when I run the analysis (selxavg3-sess), I get the following error: [...] Saving h.dat to /Freiwald/sshepherd/imaging/aboutFace/merged_Milo/bold/a_401_Av_s_task_fmov_bgrnd_icadenoise/h.dat Error using zeros Size inputs must be integers. Error in fast_selxavg3 (line 1248) hhattmp = [zeros(Navgs_per_cond,nvox); hhattmp]; % Add zero for cond 0 >> ------------------------------------------ ERROR: fast_selxavg3() failed\n a_401_Av_s_task_fmov_bgrnd_icadenoise failed [...] ============================ Looking at h.dat, I notice "Nh" is set 3.625000e+00 rather than "1" as usual. Any tips on how to debug further? *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7699

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External ROI for fcseed
by Martin Juneja 04 May '16

04 May '16

Hi all, I am trying to perform step-3 from the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… But I do not have segid because the LookUp table FreeSurfer creates after running recon-all doesn't have the area I am interested in. So I defined the ROI externally, converted it into surface using vol2surf and further into .label file using cor2label. I was wondering how can I use this externally created ROI (either in vol format, or surface format or label format) in this command: fcseed-config. I made sure that the external ROI is perfectly aligned where it was supposed to be. Thanks. MJ

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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

1 0

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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Freesurfer May 2016