[Freesurfer] Paired analysis - mismatch between matrix and contrast

Hi Freesurfer team, I'm trying to run a longitudinal group analysis (2 groups, 2 time points) using the paired analysis procedure: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis. I have followed all the instructions but when it comes to the mri_glmfit, it says that my contrast file

Re: [Freesurfer] Gaussian curvature or Mean curvature

Hi Han the ?h.curv files are the mean curvature of the white matter surface with a Gaussian smoothing kernel applied to it over space. The ?h.curv.pial is the same thing for the pial surface. The ?h.inflated.H is the (unsmoothed) curvature of the inflated surface, and the ?h.inflated.K is the

Re: [Freesurfer] Gaussian curvature or Mean curvature

Dear Bruce Fischl, Thank you for your explanation. I think I could not yet fully understand the 'curv' files. After processed this command, recon-all -s -i -all the output files were follow as, surf/?h.curv surf/?h.curv.pial surf/?h.inflated.H surf/?h.inflated.K I wonder all these output fil

Re: [Freesurfer] longitudinal spc over an ROI

Hi Rachel, yes, there is a difference if you compute SPC of the average thickness in an ROI or if you average the SPC computed on a vertex level. For the second, you can use long_mris_surf to map your third group to fsaverage and compute SPC, there is an option to write out the stack, then usi

Re: [Freesurfer] Gaussian curvature or Mean curvature

Hi Han the files ?h.curv contain the spatially smoothed mean curvature. You can compute the mean or Gaussian (or principal) curvatures of any surface using the mris_curvature command. cheers Bruce On Fri, 16 Sep 2016, Hanbyul Cho wrote: Dear FreeSurfer Team, I heard that FreeSurfer co

Re: [Freesurfer] mris_divide_parcellation

how would you like them divided? You can also use mris_make_face_parcellation to make units of approximately equal area (either in the individual or in the group) On Fri, 16 Sep 2016, Mamashli, Fahimeh wrote: Dear Freesurfer group, I am going to divide a brain parcellation into divisions usin

[Freesurfer] Gaussian curvature or Mean curvature

Dear FreeSurfer Team, I heard that FreeSurfer could calculate the Gaussian curvature and Mean curvature by vertex level. Do the computed curvature values be saved as the subject/surf/lh.curv or rh.curv files? When I prepared the generated mass-univariate data, I used the mris_preproc with [-

Re: [Freesurfer] Dev builds not found

Hi Leila we are experiencing disk problems at Martinos, which are probably causing this issue sorry, not sure when it will be fixed Bruce On Fri, 16 Sep 2016, Leila Reddy wrote: > Hi, > I get an error with mri_nu_correct.mni. I've seen on the FS wiki that this > is because I have a new versi

[Freesurfer] longitudinal spc over an ROI

Hi, I have 3 participant groups in my data set, all with 2 longitudinal time points approximately evenly spaced. I've run everyone through the longitudinal pipeline, and used the Monte Carlo simulation to find a cluster that differs in SPC between groups 1 and 2. Now I want to calculate the averag

[Freesurfer] mris_divide_parcellation

Dear Freesurfer group, I am going to divide a brain parcellation into divisions using mris_divide_parcellation. As far as I know from the help comment, this function "divides one or more parcellations into divisions perpendicular to the long axis of the label". Is there any other program that do

[Freesurfer] Dev builds not found

Hi,I get an error with mri_nu_correct.mni. I've seen on the FS wiki that this is because I have a new version of perl and that I should download the development version. However, I cannot access this page ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ (nothing happens on a linux mach

Re: [Freesurfer] Z-stat - z.mgh

Hi Doug Thanks for the information. Could you however upload it again as the files are unavailable atm? Due to congresses and holiday, I was not able to download it in time. Thank you in advance and sorry for the incovenience, Greetings Robby On 05/07/16 19:17, "freesurfer-boun...@nmr.mgh.h

Re: [Freesurfer] LGI and MATLAB

Hi Alan make sure matlab is in your path. You can check by typing: which matlab cheers Bruce On Fri, 16 Sep 2016, Alan Francis wrote: Hi Marie - I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I am unable to get FreeSurfer to recognize this (see below) , so I am

[Freesurfer] LGI and MATLAB

Hi Marie - I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I am unable to get FreeSurfer to recognize this (see below) , so I am getting an error. Is there any way to overcome this? Thanks, Alan afrancis-mac:~ afrancis$ export FREESURFER_HOME=/Applications/freesurfer af

Re: [Freesurfer] hide colored slices in 3d view?

Hi Jessica, There is no such command-line option in version 5.3. Sorry. Ruopeng > On Sep 16, 2016, at 10:44 AM, j.oschw...@psychologie.uzh.ch wrote: > > > Hi Freesurfer users, > > I wrote a script to automatize taking screenshots in Freeview. Unfortunately, > in the 3d view the colored slice

[Freesurfer] hide colored slices in 3d view?

Hi Freesurfer users, I wrote a script to automatize taking screenshots in Freeview. Unfortunately, in the 3d view the colored slices are automatically included in the picture.   Is there a way to hide them? I am using the current 5.3 version of Freesurfer.  I know that the development build incl

Re: [Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen

> > Hi Doug and all, > I just resend this email in case it did not reach, any help will be appreciated. > > Thanks for your help. I was using the preprocessed thinking that after > motion correction it would be more accurate and --init-header because they > where acquired in the same session.

Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

Hi Ajay, To open the .mgz files produced by PALM you would first load the surface in FreeView (at the top of the left panel, click on "Surface" then on the button with a "+" sign), then after the surface has been loaded, in the menu "Overlay" in the left panel, select "Load generic..." and load th