Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

Cortical Thickness of a Volume-defined ROI
by Mahtab Farahbakhsh 06 May '16

06 May '16

Dear FreeSurfer, I am trying to find the cortical thickness of my ROI which is the perisylvian region of the left hemisphere. What I did was to define a label based on the anatomical area of this region and tried to define a ROI based on this label and the command -mri_label2volume. Howevere, I am using freeview and the tutorial that I found about this issue was based on tkmedit. Would you please guide me how I should get this done? Best Regards, Mahtab Farahbakhsh.

1 0

Automatic parcellation of the postcentral gyrus
by pfannmoelj＠uni-greifswald.de 06 May '16

06 May '16

Dear Experts, in most of my subjects the cortical parcellation with the Desikan-Killiany atlas is all fine. I am especially interested in the postcentral gyrus. In several of my participants there is a typical problem with the automatic parcellation in this region. About half the postcentral gyrus is parcellated correctly (the lower half), but the upper half is shifted to a posterior part of the brain and the upper half of the postcentral gyrus is parcellated as the precentral gyrus. Attached you find a typical example, one hemisphere is parcellated correctly (left_hemisphere.jpg), the other one shows the problem (right_hemisphere.jpg). The postcentral gyrus is shown in red and the precentral gyrus in blue. The only difference that I can spot is in the anatomy of the superiorparietal and supramarginal regions. These regions are disconnected in the left hemisphere, but have a gyrus which connects them in the right hemisphere. May that cause the difference in the parcellations? Yours pfannmoe

2 1

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

5 13

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

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