Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

glmfit --table (by tract TRACULA outputs)
by Pedro Rosa 05 May '16

05 May '16

Dear list, I am trying to use mri_glmfit to run statistics on TRACULA outputs (by tract), as suggested by the wiki ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics) I used the following command line: mri_glmfit --glmdir ilf.glmdir --table ilf.txt --fsgd sociodemo.fsgd --C 2G1V-1100.mtx It ends without errors. How should I proceed with correction for multiple comparisons, as I cannot use Monte Carlo? Best, Pedro.

1 0

no recon button
by Burke,Sarah E 05 May '16

05 May '16

Hello, I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux. I have no recon button. What should I do? Thank you

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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

1 0

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

2 8

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

2 1

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

3 4

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

2 1

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

2 1

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

1 0

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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