Re: [Freesurfer] Thalamic segmentation tool: question about input files from recon

I think it has to go through the whole recon as it uses wmparc.mgz and that is one of the last things created On 1/5/2023 4:16 AM, Verónica E wrote: External Email - Use Caution Dear all, I am planning to run the thalamic segmentation (as implemented on FreeSurfer 7.1). The data has

Re: [Freesurfer] Thalamic segmentation error

External Email - Use Caution Thank you Eugenio and R. It works great. On Wed, Oct 19, 2022 at 4:04 PM fsbuild wrote: > > You shouldn’t be getting errors about libcuda (which we do not support). > > If you have not already done so, please try the script we provide to > install th

Re: [Freesurfer] Thalamic segmentation error

External Email - Use Caution You shouldn’t be getting errors about libcuda (which we do not support). If you have not already done so, please try the script we provide to install the Matlab runtime environment, $ cd $FREESURFER_HOME/bin$ sudo FREESURFER_HOME=$FREESURFER_HOME ./f

Re: [Freesurfer] Thalamic segmentation error

External Email - Use Caution Hi Eugenio - Thanks for your reply. We have a Linux Tech. He installed it for me. Should I reinstall the runtime ? Thanks, Alan On Tue, Oct 18, 2022 at 2:59 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mgh.harvard.edu> wrote: > Dear Alan, > Ho

Re: [Freesurfer] Thalamic segmentation error

Dear Alan, How did you install the runtime? Did you follow the instructions in the wiki? Cheers, /Eugenio Juan Eugenio Iglesias www.jeiglesias.com On Oct 18, 2022, at 2:37 PM, Alan Francis mailto:alandarkene...@gmail.com>> wrote: External Email - Use Caution

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] Thalamic segmentation in FS voxel space

Dear George, The volumes in the text files come from soft segmentations at high resolution. There are two factors contributing to the discrepancies: 1. The downsampling to 1mm isotropic 2. The use of soft vs hard segmentations when computing volumes. For example: if you’ve got 100 voxels w

Re: [Freesurfer] Thalamic Segmentation of Post Contrast MRI

Dear Baris, It’s hard to tell without seeing images… Would you mind sharing a scan? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of barış genç Reply-To: Freesurfer support list Date: Sunday, May 24,

Re: [Freesurfer] thalamic segmentation analysis

Hi VP you need to give us more information! What is going wrong? What kind of system are you installing/running on? Send us the commands you are running and their output including any error messages. cheers Bruce On Sat, 28 Mar 2020, Parisi Veronica wrote: External Email - Use

Re: [Freesurfer] Thalamic segmentation

External Email - Use Caution Dear Zheng One of the other developers can help you with Freeview. But, as a workaround, you can always use an earlier version of Freeview, and load the lookup table of the Dev version. Cheers Eugenio Sent from mobile, please excuse brevity and typos

Re: [Freesurfer] Thalamic segmentation questions

External Email - Use Caution Dear Manoj, First question: The one without the suffix is defined at higher resolution, on a voxel grid that does not correspond to the standard FS space (where norm.mgz, aseg.mgz, etc. live). The one with the suffix lives on the voxel grid of norm.m

Re: [Freesurfer] thalamic segmentation

>> Hi Vinny, >> The anatomical definitions can be found in the paper, which is open >> access (see Table 2): >> https://www.sciencedirect.com/science/article/pii/S1053811918307109 >> Kind regards >> Eugenio >> >> >> >> Sent from my phone

Re: [Freesurfer] thalamic segmentation

> > > > > > > From: Vinny K > Sent: Monday, September 10, 10:35 > Subject: Re: [Freesurfer] thalamic segmentation > To: freesurfer@nmr.mgh.harvard.edu > > > External Email - Use Caution > Hi, > > I ran recon-all to generate the required files fo

Re: [Freesurfer] thalamic segmentation

From: Vinny K Sent: Monday, September 10, 10:35 Subject: Re: [Freesurfer] thalamic segmentation To: freesurfer@nmr.mgh.harvard.edu External Email - Use Caution Hi, I ran recon-all to generate the required files for the thalamic segmentation tool (http://freesurfer.net/<h

Re: [Freesurfer] thalamic segmentation

External Email - Use Caution Hi, I ran recon-all to generate the required files for the thalamic segmentation tool (http://freesurfer.net/fswiki/ThalamicNuclei) using the latest development version of Freesurfer (06/09/2018) linux-cent06. The segmented thalamic nuclei were visual