[Freesurfer] Thalamic segmentation with FGATIR not running

External Email - Use Caution Hi While doing thalamic segmentation with FGATIR additional volume, I am getting an error that "BIAS field corrected version of additional volume found; no need to recompute error: No such file or directory error: WARNING: 419053 NaNs found in volume t

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

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

External Email - Use Caution Dear all, I am planning to run the thalamic segmentation (as implemented on FreeSurfer 7.1). The data has been already preprocessed with FreeSurfer 5.3, but I want to rerun the recon step on the newer FreeSurfer version. My question is, which recon

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

[Freesurfer] Thalamic segmentation error

External Email - Use Caution Hi Eugenio - Hope all is well. I am running FS 7.2. I have installed the MATLAB Runtime 2014b. However when I run the thalamic segmentation routine I get this error. Please help. Thanks, Alan copernicus:~/IMAGING> segmentThalamicNuclei.sh 973770 Set

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

[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] Thalamic segmentation in FS voxel space

"Thomas, George" Reply-To: Freesurfer support list Date: Thursday, April 15, 2021 at 07:07 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Thalamic segmentation in FS voxel space External Email - Use Caution External Email - Use Caution D

[Freesurfer] Thalamic segmentation in FS voxel space

External Email - Use Caution Dear All, I have run segmentThalamicNuclei.sh on a set of subjects with 1mm isotropic T1 images. I need to convert these labels into volumetric space for further analysis so have been using the output with the FSvoxelSpace suffix and converting .mgz

Re: [Freesurfer] Thalamic Segmentation of Post Contrast MRI

, 2020 at 06:21 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Thalamic Segmentation of Post Contrast MRI External Email - Use Caution Dear FreeSurfer Experts, I have a data set (control and patients) that has 3DT1 , acquired on 3 T Philips Achieva scanner

[Freesurfer] Thalamic Segmentation of Post Contrast MRI

External Email - Use Caution Dear FreeSurfer Experts, I have a data set (control and patients) that has 3DT1 , acquired on 3 T Philips Achieva scanner after post contract (Gadolinium). Can I use his data set to measure the thalamic nuclei segmentation or amygdala segmenta

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

[Freesurfer] thalamic segmentation analysis

External Email - Use Caution Hi there, I have been trying to learn and set-up Freesurfer for a research project I am working on, but I am having trouble with the set-up/installation process. Once Freesurfer is set-up, I will be using it to measure thalami and define their sub n

Re: [Freesurfer] Thalamic segmentation

: [Freesurfer] Thalamic segmentation External Email - Use Caution Hi Expert, In the latest version of FS, I have segmented the thalamic successfully. But I can't use Freeview to show the segmentation map. There is an error :"freeview: /usr/lib/libpng15.so.15:version 'PNG

[Freesurfer] Thalamic segmentation

External Email - Use Caution Hi Expert, In the latest version of FS, I have segmented the thalamic successfully. But I can't use Freeview to show the segmentation map. There is an error :"freeview: /usr/lib/libpng15.so.15:version 'PNG15_0' not found (required by /opt/freesurfe

Re: [Freesurfer] Thalamic segmentation questions

Harvard Medical School http://www.jeiglesias.com From: on behalf of Manoj Saranathan Reply-To: Freesurfer support list Date: Tuesday, 29 January 2019 at 19:15 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Thalamic segmentation questions External Email - Use C

[Freesurfer] Thalamic segmentation questions

External Email - Use Caution The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice calcu

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