[Freesurfer] red and blue gradient color map for freeview

Hi all, I'd like to have a freeview color map that has both a red-yellow gradient and a blue-light blue gradient (the typical colors for positive and negative fcMRI correlations) and ideally no color for 0... None of the standard color maps in freeview work well and I can't seem to find one

Re: [Freesurfer] Freesurfer 6.0?

Did you receive a reply/ Any news update for 6.0 release? On Mon, Jul 25, 2016 at 1:01 PM, Trisanna Sprung-Much < trisanna.sprung-m...@mail.mcgill.ca> wrote: > > Hi there > > Do we have a potential date for the Freesurfer 6.0 release? I was told I > would want to re-run all my subjects to

[Freesurfer] when to -qcache in longitudinal processing

Hello Freesurfers, My ultimate goal is a MLE analysis of 2 groups (n~25) at 2 time points. I have followed the longitudinal processing stream (cross, base, long) although only ran -qcache at the cross stage. Do I need to add this flag to the base and/or long recon-all command? Or is the same

Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

Dear Anastasia, I have also uploaded the file with the problem (22995_EM.zip), and this is how my config file looks like after modifications: set subjlist = (22995) set pathlist = (fmajor_PP) set ncpts = (7) set reinit = (1) Thanks again! Best Wishes, Elijah -- Elijah Mak PhD Candidate

Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

Hi Elijah - You add "set reinit =1" to the config file, (and remember to set the pathlist and subjlist to only what you want to rerun), and then rerun the -prior and -path steps in that order. Best, a.y On Thu, 18 Aug 2016, Elijah Mak wrote: Thanks for the tips on reinitialisation of

Re: [Freesurfer] label analysis

Use mris_anatomical_stats On 8/18/16 9:53 AM, Raffaele Dubbioso wrote: Dear Freesurfer team, I'm working on structural data analysis using Fressurfer. I have drawn my own labels and now I'd like to get data like thickness, curvature, folding index in the same way that I usually get when I

Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

Hi Elijah - It looks like the CVS case needs to be reinitialized. In principle you're right that if the registration is good this shouldn't be a problem. It's hard to tell what might've caused this in an individual case without looking at the data. If you want me to look into it you can

Re: [Freesurfer] FSFAST ROI atlas

Yes, the Gordon parcellation paper: http://www.ncbi.nlm.nih.gov/pubmed/25316338 --  Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine

Re: [Freesurfer] FSFAST ROI atlas

Hi Michael- Thanks very much for the file. Is there published paper or other documents that I could use as reference for these annotation? Cheers, Sabin Khadka On Wed, Aug 17, 2016 at 12:53 PM, Harms, Michael wrote: > > They are attached (assuming that the FS list allows

[Freesurfer] label analysis

Dear Freesurfer team, I'm working on structural data analysis using Fressurfer. I have drawn my own labels and now I'd like to get data like thickness, curvature, folding index in the same way that I usually get when I run the aparc.stat function. Can you please help me how to solve this problem?

Re: [Freesurfer] Error with long_mris_slopes: Surface files do not exist

Hi Nick, I don’t understand what you are trying to do. I don’t think ?h.surface is a valid file (it is not created or used by freesurfer). Surfaces are for example ?h.white or ?h.pial. Also you say that thickness files exist and that the long_mris_slopes analysis worked for thickness. You