[Freesurfer] FS 5.3 and OS X 10.11

Hi, On the download page it mentions that Freesurfer v5.3 is not compatible with OS X 10.11 because of an implementation of SIP. As a test, I have run a few subjects with v5.3 under OS X 10.11.3 with SIP enabled but was unable to see any problems, with all test subjects completing without erro

Re: [Freesurfer] Tracula_weighted dti metrics values

You need to specify some volume to display the paths over. The paths are just text files with a list of point coordinates, so it has no idea in what space to display them if you don't specify a volume. Check the tracula tutorial, too. On Tue, 9 Feb 2016, Karuna Subra wrote: Hi Anastasia,

Re: [Freesurfer] Fwd: 3D viewing ROIs by Freeview

Hi Faezeh, What do you mean by 3D brain map? Is it a 3D surface? What is the format of the ROIs you are trying to load? Ruopeng On 02/09/2016 02:01 PM, Faeze Vedaei wrote: Hello Freesurfer experts, I am Faezeh Vedaei a research assistant in a neurology lab at the Michigan State University.

Re: [Freesurfer] Tracula_weighted dti metrics values

Hi Anastasia, Yes, it's the one that came with freesurfer 5.3. Is it possible to use the GUI to get waypoint to display the paths rather than command line? I have all the mean path outputs in the stats folder as shown here but somehow am getting this weird error below. Thanks. Karuna On Fri,

Re: [Freesurfer] Combining lh. and rh. surfaces

Hi Jesu, Thanks very much for your reply. I have downloaded SIMNIBS and will try to use it to do this. Is there a tutorial you recommend to do this specific thing that I have asked? Thanks! Maheen On Fri, Feb 5, 2016 at 1:39 PM, Jesu Kiran Jk wrote: > Hi Maheen, > > I have been using SIMNIBS

[Freesurfer] Fwd: 3D viewing ROIs by Freeview

Hello Freesurfer experts, I am Faezeh Vedaei a research assistant in a neurology lab at the Michigan State University. In my project I want to have a 3D view of ROIs which I just extracted by AFNI, after I executed recon-all. I would like to help me how can I overlay some specific ROIs on a 3D bra

Re: [Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview)

I just did a tst of mri_convert of freesurfer v5.3 on my Ubuntu 14.04 machine and it ran successfully. Freeview also ran (after typing the libjpeg symlink command). Can you provide any error or terminal output information? -Zeke On 02/08/2016 12:41 PM, Veronica.Popescu wrote: > Dear all, > I h

[Freesurfer] tkregister visualization issue

Dear Freesurfer team, I encountered a visualization error with tkregister-sess after trying to look at the overlays of my 1st level analysis in a standard fMRI block designed localizer. tkregister loads without errors (menu plus window) but only very faint and small colored dots are visible, n

[Freesurfer] segmentation errors in subject with severe atrophy

Dear all, We are working on editing the segmentation of a subject with severe atrophy due to a seizure event that occurred during infancy. In portions of the parietal and frontal lobe the atrophy is so severe that freesurfer can't find any WM or GM. Is there a way to manually fill in the GM so that

Re: [Freesurfer] Processing of young children using Freesurfer

Hi Bruce, thanks for the reply. Here comes the output (see attached). I just downloaded the VM with freesurfer from your website, fyi. Yours Frank PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim H

[Freesurfer] fwhm issue with mri_glm-sim

Dear FS team, I am running a surface based analysis on GWR on a group of 203 subjects. I generated left and right GWR maps, smoothed with a Gaussian kernel of FWHM 15 mm. However when I try to run the multiple comparisons correction analysis (mri_glmfit-sim --glmdir lh.w-g.pct_aesint.15.glmdir --c

Re: [Freesurfer] Processing of young children using Freesurfer

hmmm, this doesn't seem to have to do with your data but maybe is an installation problem? It says it failed but doesn't give an error message, which is unusual. Can you try just typing in directly: cd /media/sf_cdh_ventrikel/test_002/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 5

Re: [Freesurfer] Processing of young children using Freesurfer

Hi again, just an update, I treid this all again with an older child (109 years) but same thing happens. Logfile attached. Yours Frank PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg Uni

[Freesurfer] retinotopy analysis: wedge position, angle offset, tksurfer

Hello everyone, I've analyzed my polar retinotopy data (2 runs with clockwise and counterclockwise wedge rotations) using FsFast. To better understand the analysis, I'd be very grateful if you could help me with the following questions: 1. I understand that freesurfer assumes that the rotating w

Re: [Freesurfer] Reading values from overlays with PETcoreg

Hello Doug, Thanks for your answer! I already tried this workflow but basically I am interested in a surface-based analysis. Is it possible by using this workflow to get the any stats.dat just for surface-ROIs? Best, Benjamin Spurny On Fr, 29.01.2016, 01:34, Douglas N Greve wrote: > > > On 01/2

[Freesurfer] Processing of young children using Freesurfer

Hi, I am currently working on a project involving brain morphometry of 2 year old children. We are interested in segmenting the ventricle and I tried to run freesurfer using the standard recon-all -all for a first test. Unfortunately, freesurfer reports an error (see attached log file). I als