Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution MCRv84 looks like it should run on MacOS 10.13, so in a new terminal window, I would install it directly into the freesurfer distribution with, $ export FREESURFER_HOME=/Applications/freesurfer/7.2.0$ cd $FREESURFER_HOME$ rm -rf MCRv84 $ cd bin $

Re: [Freesurfer] Thalamic nuclei exited with ERRORS

External Email - Use Caution Hi all, Just bumping this one up. Any help would be really appreciated. Thanks in advance, Yann > On 27 Aug 2022, at 10:47 am, Yann Quidé wrote: > > Hi team, > > I have been having troubles with processing my scans for thalamic subnuclei. > In

Re: [Freesurfer] segment_subregions failed

Greetings, I am having some trouble reproducing that error. Could you send me the commit number of the git reop you cloned? Jackson Nolan, BSc - Programmer Laboratory for Computational Neuroimaging (LCN) Athinoula A. Martinos Center for Biomedical

[Freesurfer] mri_binarize error for thalamic nuclei during trac-all prep

External Email - Use Caution Hi Freesurfer Developers, I'm trying to troubleshoot an error message during TRACULA preprocessing that seems to be related to the mri_binarize command used to create the /dlabel/anatorig/aparc+aseg+thalnuc.nii.gz file. I'm using FS v7.3.2 on OS

Re: [Freesurfer] FSFAST first level covariates

External Email - Use Caution Great, thanks so much Doug- this setup makes sense to me. However, isn’t it a problem that the brain regions associated with the contrast for -a 3 and the contrast for -a 4 would be the same for trials that subjects rate as 1 (self-relevant) vs 0

Re: [Freesurfer] samseg inputs

Hi Dilek, I've actually run SAMSEG-lesion on some gadolinium-enhanced scans in the paper. Look at the top row of Fig. 7 ("T1c") and at the "MSseg" dataset. I did not check the performance of the method on such data. We also don't distinguish between enhanced and non-enhanced lesions. I would

[Freesurfer] Freesurfer VM package

External Email - Use Caution Hello, I want to install the VM Package of Freesurfer and was asked for a passcode to upack the zip file. Could you provide me one? Best Kolja ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Van Essen/Glasser Lab Connectome Post-Doc Opportunity

External Email - Use Caution Hi FreeSurfer Users, We have a Connectome-related Post-Doc position available immediately in the Van Essen/Glasser lab. Please see the below posting. Feel free to forward to anyone you know who might be interested. Thanks, Matt. Postdoctoral

[Freesurfer] samseg inputs

External Email - Use Caution Hello dear all, I want to use Freesurfer-Samseg for MS lesion segmentation(cross-sectional). I have read the paper, accordingly I want to try the t1-flair combination in terms of the accuracy. Do you have any experience with T1 images with contrast