[Freesurfer] BERT - Example of segmentation

External Email - Use Caution Dear Freesurfer team, It is my first time editing wm segmentation (white matter segmentation errors + topological errors). I wonder if there is a good tutorial on which I could rely. Also, I have read there is an example of segmentation that comes wi

Re: [Freesurfer] BERT - Example of segmentation

External Email - Use Caution Hi Rosie, > It is my first time editing wm segmentation (white matter segmentation > errors + topological errors). > > I wonder if there is a good tutorial on which I could rely. > There are a few tutorials that may be helpful (a full list of tutoria

Re: [Freesurfer] BERT - Example of segmentation

External Email - Use Caution Thank you! Rosie On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton wrote: > External Email - Use Caution > > Hi Rosie, > > >> It is my first time editing wm segmentation (white matter segmentation >> errors + topological errors). >> >> I wonder

Re: [Freesurfer] BERT - Example of segmentation

External Email - Use Caution Hi Paul, Not sure what command I should run when I edit the brainmask because the pial got too much. Kind regards, Rosie On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton wrote: > External Email - Use Caution > > Hi Rosie, > > >> It is my firs

Re: [Freesurfer] BERT - Example of segmentation

External Email - Use Caution Hi Rosie, I'm going to have to defer to others about questions on manual editing.. I've never done it! Sorry, -Paul On Thu, Jul 8, 2021 at 1:27 PM Rosalia Dacosta Aguayo wrote: > External Email - Use Caution > > Hi Paul, > > Not sure what

Re: [Freesurfer] BERT - Example of segmentation

External Email - Use Caution The troubleshooting tutorial suggest running freeview -v pial_edits_before/mri/T1.mgz \ pial_edits_before/mri/brainmask.mgz \ -f pial_edits_before/surf/lh.white:edgecolor=yellow \ pial_edits_before/surf/lh.pial:edgecolor=red \ pial_edits_before/surf

[Freesurfer] Freeview filled in labels along with their outlines

External Email - Use Caution Hi, In freeview, is it possible to view a collection of labels with different filled in colors, as well as their outlines? So, a combination of the filled in and outline only modes? Best, Prad ___ Freesurf

Re: [Freesurfer] Freeview filled in labels along with their outlines

It is possible to show outline only but not combined with filled ones. Ruopeng On Jul 8, 2021, at 5:02 PM, Pradyumna Bharadwaj mailto:p...@email.arizona.edu>> wrote: External Email - Use Caution Hi, In freeview, is it possible to view a collection of labels with different filled in

Re: [Freesurfer] TRACULA: No b0info.dat file / error epidewarp.fsl

External Email - Use Caution Dear Anastasia Thanks for the information. I do not want to start with the DICOMs and therefore the difference in TE cannot be extracted. Is there an easy work around to provide —tediff or the file b0info.dat to trac-all -prep? I tried to define —ted