[Freesurfer] Recon Reprocessing Issues

Hi Freesurfer People,I’m working on a 2015 Macbook Pro with OS X El Capitan version 10.11.2 and I have System Integrity Protection disabled (though I hadn’t experienced any issues that could have been a result of that function). Everything in FreeSurfer works fine for me—I ran recon-all and success

Re: [Freesurfer] TRACULA messy tracts

Hi Jacek - Yes, these definitely look all over the place! It would help to get a screenshot of your subject's FA map and some more info on the acquisition. For example, is there any head motion? What's the voxel size and the number of gradient directions? Best, a.y On Sun, 14 Feb 2016, Jac

Re: [Freesurfer] path.pd.trk format

Hi Noam - You can read the .trk file with trackvis. It contains all the path samples that are added up to created the probability distribution of the path. Please keep in mind, however, that this .trk file is just meant for generating stats and not for visualization, so these are not the usual

Re: [Freesurfer] TRACULA Adding a new tract to the finished analysis

Hi Deniz - You can definitely only run a subset of the tracts, by using the "pathlist" variable in your configuration file and setting it to only the tracts you want. This will reconstruct these specific tracts, and then it will regenerate the merged_... file to include them together with any

Re: [Freesurfer] TRACULA messy tracts

Hi Deniz - That cingulum looks way more inferior than it should be. It's hard to tell without being able to see the coronal view. It would make sense to reinitialize a couple of the tracts if the rest of the tracts in the subject look fine, but if they're all shifted inferior then it's a more

[Freesurfer] Generating Masked Aseg Segmentation Volumes

Hi Freesurfer Team, I'm attempting to calculate the volume of hippocampal subfields (e.g., CA1-3, DG) in the anterior (head), middle (body), and poster (tail) subregions of the hippocampus. I have manually determined the boundaries for head/body/tail using standard anatomical landmarks and included

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

Hi Ankita, Did you get this error with only one subject, or with several different subjects? Have you checked your pial surface with freeview or tkmedit? No issue there? If your pial surfaces are fine and you get the issue for all the subjects you tried, send me a sample of pial surface + T1.m

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

That's perfect. I think that solved the issue. It was not referencing the matlab files from freesurfer I guess. Thank you so much! It seems to be processing now! Thanks! Ankita On Sat, Mar 5, 2016 at 8:05 AM, Ankita Chatterjee wrote: > Thank you for the pointer Woo-Suk. So to do that, I just do

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

Start matlab and just add /usr/local/freesurfer/matlab folder of your linux system to "set path" function (click in matlab's menu) of matlab environment. 2016. 3. 6. 오전 1:07에 "Ankita Chatterjee" 님이 작성: > Thank you for the pointer Woo-Suk. So to do that, I just do an EXPORT PATH > on Matlab? I am n

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

Thank you for the pointer Woo-Suk. So to do that, I just do an EXPORT PATH on Matlab? I am not very familiar with linux... Thanks! Ankita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesur

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

One possible solution is adding ../freesurfer/matlab to your matlab's set path. Regards Woo-Suk Tae Seoul, Korea Woo-Suk, Tae Ph.D. Research Professor Brain Convergence Research Center, Medical Research

Re: [Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

can you send us the recon-all.log file? cheers Bruce On Sat, 5 Mar 2016, Ankita Chatterjee wrote: > Hello FS experts,I am a bit stuck and was hoping for some advice! > > I am using Matlab Student version for my research and was trying to > determine local gyrification index on some samples that

Re: [Freesurfer] recon-all and local Gyrification Index

Hi Ankita have you tried contacting mathworks? cheers Bruce On Sat, 5 Mar 2016, Ankita Chatterjee wrote: Hello Freesurfer experts - raising this question once more. Also if I downloaded a trial version of Matlab to see how it integrates, but am unable to activate it. Anyone with similar issu

[Freesurfer] recon-all -lgi issue with MATLAB Student version - Help!

Hello FS experts, I am a bit stuck and was hoping for some advice! I am using Matlab Student version for my research and was trying to determine local gyrification index on some samples that I have processed via the recon-all -all step. When I run recon-all -lgi on my subject, it starts up, is ab

Re: [Freesurfer] recon-all and local Gyrification Index

Hello Freesurfer experts - raising this question once more. Also if I downloaded a trial version of Matlab to see how it integrates, but am unable to activate it. Anyone with similar issues? When I run my recon-all - lgi command, it starts up and fails with an error that MATLAB has a licensing erro