[Freesurfer] parallel recon-all using T1,T2 images

External Email - Use Caution Hello Freesurfer experts I am trying to recon-all using T2 images as well to improve pial surfaces. Does anyone know how to use GNU Parallel in bash to run the following commands in parallel? recon-all -subject subjectname -i /path/to/T1w.nii -T2 /pat

Re: [Freesurfer] parallel recon-all using T1,T2 images

External Email - Use Caution That is a single command. How can you run a single command in parallel? You can add the -parallel flag to get freesurfer to run recon-all in parallel threads. On Thu, Apr 27, 2023 at 8:16 AM Toshiharu Kamishikiryo wrote: > External Email -

Re: [Freesurfer] contrast-FSGD question

External Email - Use Caution Bumping this up. Thanks so much! Best, Fred > On Apr 24, 2023, at 8:52 PM, Fred d'Oleire Uquillas > wrote: > >  > Dear Fs support, > > If I have the following FSGD with 4 classes and 3 variables, and I'd like to > run an interaction of ROIa x R

Re: [Freesurfer] EasyReg for group-average template?

External Email - Use Caution Hi Eugenio, Thanks for your reply. Just to check if I've understood correctly, these can be the steps by using mri_easyreg: *Linear (with --affine-only):* 1. Register all the subjects to the MNI (subj_to_MNI_lin_1) 2. Average the subj_to_MNI_li

[Freesurfer] Fwd: questions about mri_normalize

External Email - Use Caution Dear experts, I have been using the mri_normalize in FSv7.3.2 to standardize the intensity of FLAIR images , and I've observed that increasing the sigma parameter up to 25 is effective in improving the quality of the normalized images for noisy datasets

Re: [Freesurfer] parallel recon-all using T1,T2 images

External Email - Use Caution Thanks for pointing that out, sir. 2023年4月27日(木) 16:15 Toshiharu Kamishikiryo : > Hello Freesurfer experts > > I am trying to recon-all using T2 images as well to improve pial > surfaces. Does anyone know how to use GNU Parallel in bash to run the > f

[Freesurfer] visualization, heatmap

External Email - Use Caution Dear Freesurfer team, I noticed that some studies/publications add figures with heatmaps to visualize the significant cortical results (after correction), others do not. We tried to use the heat map (from yellow/red to dark blue/light blue) to visuali

Re: [Freesurfer] FSFAST: wrong brain mask in preproc

External Email - Use Caution Thank you for clarifying. Elmira On Wed, Apr 26, 2023 at 6:44 PM Douglas N. Greve wrote: > External Email - Use Caution > > Yes, this is the expected behavior, ie, it should cover only subcortical > GM regions. It is expected that cortical r

Re: [Freesurfer] visualization, heatmap

External Email - Use CautionHey Eszter,Have you tried loading in the “sig.masked.mgh” file that’s in your contrast results folder? It should show only the significant cluster after multiple comparisons correction with the original colorbar gradient inside.Best,FredOn Apr 27, 2023, a