Re: [Freesurfer] creating. or replacing a label of choice in aseg atlas

Adding ROIs in fsaverage will not cause them to appear in the aseg.mgz volume; fsaverage is not the atlas. If you have your ROIs in fsaverage space, you can map them to the individual via a linear or nonlinear mapping, but the accuracy will be debatable. You don't need to merge them with the

Re: [Freesurfer] Integrating glmsingle with freesurfer and mri_glmfit

No, I think that should work fine. On 5/16/2022 3:49 PM, Lauri Tuominen wrote: > External Email - Use Caution > > Dear FreeSurfer experts, > > I would like to use mri_glmfit to do 2nd level random effects analysis on > fMRI data I fit with GLMsingle: >

Re: [Freesurfer] Perform aseg in Freeview

Nope, you have to use the command line. If you have a T1weighted image, you can just recon-all -i t1w.mgz -s subject -all The aseg will be in subject/mri/aseg.mgz There are a few other options for this as well, like samseg --i t1w.mgz --o samsegdir The seg will be in samsegdir/seg.mgz Or you can

[Freesurfer] Freesurfer Passcode

External Email - Use Caution Hello all, I would like to request for a passcode for

Re: [Freesurfer] Permission denied error from -localGI

Just closing this thread: we have solved it in https://forum.freesurfer.net/t/permission-denied-error-from-localgi/62 Thanks, Tashrif ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Integrating glmsingle with freesurfer and mri_glmfit

External Email - Use Caution Dear FreeSurfer experts, I would like to use mri_glmfit to do 2nd level random effects analysis on fMRI data I fit with GLMsingle:

[Freesurfer] Infant FreeSurfer: volumes extraction without surface

External Email - Use Caution Hi FreeSurfer team, I've been using Infant FreeSurfer for several very young subjects and it works pretty well. But after reviewing the generated surfaces, it looks like pial surface is not extended to fit the cortical grey matter as you can see

[Freesurfer] Perform aseg in Freeview

External Email - Use Caution Hello, brand new to this software and community so I apologize if this is a dumb question or if I’m asking it through the wrong channels. I understand that Freeview is just a visualizer for Freesurfer, but since I just want to use it to

[Freesurfer] Passcode for FreeSurfer VM

External Email - Use Caution Dear all, I hope you are doing well. I am an intern at the University of Gothenburg, Sweden, could you please provide me with a passcode for FreeSurfer VM image? I would like to use this version:

Re: [Freesurfer] creating. or replacing a label of choice in aseg atlas

External Email - Use Caution Thank you for the response, Yes editing the aseg.mgz in the fsaverage directory with the custom roi's. The purpose of doing it on the aseg.mgz in the fsaverage directory is- so that we can use these roi's once for all for every subsequent subject