Re: [Freesurfer] FreeView issue!

External Email - Use Caution Just wondering if you already tried using bash to setup the environment.  - R. %] bashbash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh Setting up environment for FreeSurfer/FS-FAST (a

Re: [Freesurfer] FreeView issue!

External Email - Use Caution Hi Ruopeng Thanks for your quick response. If I use that I still get the similar error: BT136080:~ bajsah$ $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview Segmentation fault: 11Segmentation fault: 11 Sahil On Fri, Jul 16, 2021 at 1:23 PM Wang

Re: [Freesurfer] FreeView issue!

What if you run: $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview -f fsaverage/surf/lh.inflated > On Jul 16, 2021, at 1:07 PM, Sahil Bajaj wrote: > > External Email - Use Caution > > > Hi everyone, > > I am having following error while opening freeview in terminal: > >

[Freesurfer] FreeView issue!

External Email - Use Caution Hi everyone, I am having following error while opening freeview in terminal: BT136080:01_Project_FreeSurfer bajsah$ freeview -f fsaverage/surf/lh.inflated /Applications/freesurfer/7.1.1/bin/freeview: line 2: 27046 Segmentation fault: 11 $FREESURFER_

[Freesurfer] Fwd: Fwd: Yeo atlas for children!

External Email - Use Caution Dear Thomas and FreeSurfer experts, Here I am just reposting my question below - just in case this was missed by the experts. Any help would be really appreciated. -- Forwarded message - From: Martin Juneja Date: Sat, Jul 10, 2021 at

[Freesurfer] Claustrum segmentation

External Email - Use Caution ?Hi all, I was wondering if any of you guys have had experience wanting to segment the claustrum in 3T scans. It is a label that is found in Freesurfer, but isn't reported in the stats. Is that something that Freesurfer hopes to develop. Or is ther

Re: [Freesurfer] Mac OS problem with .pial files

On Big Sur you will need to grant permissions to read and write for all the freesurfer binaries. Have you done so? Also, you can download the latest standalone build of freeview for macOS here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Ruopeng On Jul 16, 2021, at 10:13 AM, TILSL

Re: [Freesurfer] Thalamic segmentation error Big Sur

Hi Daniel This error is intriguing because the code did run for a while… Is it possible that you ran out of RAM memory? How much RAM does your machine have? (you can find it by clicking on the apple on the top left corner and then “about this Mac”) Cheers, /E Juan Eugenio Iglesias Senior resea

Re: [Freesurfer] /usr/pubsw reference in 7.1.1

External Email - Use Caution I'm not familiar with FLICA, but you should be able to make a symlink for compatibility issues like this. First, backup the original tksurfer: mv $FREESURFER_HOME/bin/tksurfer $FREESURFER_HOME/bin/tksurfer.orig Then: ln -s $FREESURFER_HOME/bin/tksurfe

[Freesurfer] Mac OS problem with .pial files

External Email - Use Caution Hello, I have recently changed from Linux to Mac OS (Big Sur) and have problems with loading lh.pial and rh.pial files on the Mac system. The files were created using the recon-all command on the Linux system, this finished without error. But I wonde

Re: [Freesurfer] FIR analysis and task regressor (continued) & slice-timing correction

External Email - Use Caution Hi Doug, I run into some questions while trying to do this analysis: How do you set up the contrast you suggested? Since there is no paradigm file, I don't know what I should enter as conditions. But on the other hand, I automatically get ces.nii.g

[Freesurfer] Follow-up: PVC to calculate myelin maps

External Email - Use Caution Dear FS-experts, I want to create myelin maps out of T1w/T2w contrasts and I have already read this e-mail conversation from the archive:

[Freesurfer] Thalamic segmentation error Big Sur

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to segment thalamic nuclei, as described by the tutorial page (https://secure-web.cisco.com/1F9Cs4OMcQ2PV75K6Q0sKfyHoo5UBJNkIWoWVANuievmgb7YVmB72kOrHuNn1V8uoNhZN-KHe4ok9nSjzkSzoyH5n058ic0lLqwrMVHZ1ozpd7WV13-

Re: [Freesurfer] FIR analysis and task regressor (continued) & slice-timing correction

External Email - Use Caution Yes, that's exactly what I want. Thanks for the explanation! Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve Gesendet: Donnerstag, 15. Juli 2021 18:05 An: freesurfer@nmr.mgh.harvard.edu