Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all

Hi Nick, The option -talairach-nu is not recognized in version v5.1.0. How can I proceed now? Ed On 16 Apr 2012, at 17:32, Nick Schmansky wrote: > Ed, > > Hi, no there is not an option to switch them. The nu correct stage in > 5.1 needs the talairach to run. > > However, if your intent is to

[Freesurfer] How to create a circle ROI centered at certain coordinate?

Dear Freesurfer experts, Recently, I was creating ROI. But I just knew how to create it manually as this website introduce: http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit. Does Freesurfer provide the way to create ROI by using of certain coordinate? That is, if I know the MNI or Talai

Re: [Freesurfer] Segmentation

Hi Jordan, I'm not sure I understand your question. If you run -make all, it will run recon-all again starting at the earliest step in which there are files that were changed that affect that step. It will run all the way through to the end as each step affects the next one. This will change you

Re: [Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all

Ed, Hi, no there is not an option to switch them. The nu correct stage in 5.1 needs the talairach to run. However, if your intent is to get a better talairach result by using the nu corrected input (as it did prior to v5.1), then you can do the following: recon-all -s subjid -motioncor -talai

Re: [Freesurfer] Longitudinal Edits, skull strip and wmcp, how to do this longitudinally

Hi Mark, did you see our wiki page about longitudinal editing? It discusses these things in detail (e.g. where to edit what): http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits also the tutorial has several examples on how to edit: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Long

[Freesurfer] Segmentation

Hi, We're trying to edit the aseg segmentation and reconstruct it.  If we run 'recon-all -s subject -make all' does that depend on any information from the surfaces or brainmask volume, or are the stats independent of that? Thank you,   Jordan Pierce Graduate Student Behavioral and Brain Scie

[Freesurfer] WM modification

Dear freesurfers,May be a silly question:I'd modified the wm.mgz using the lastest current version of FS as suggested in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits?highlight=%28matter%29%7C%28White%29Is there any output on FS that quantifies the lesions as volume or someth

[Freesurfer] QATools

Dear FreeSurfer expert, I am trying to run QA tools for verifying all steps of the FreeSurfer recon-all stream. I am working with FreeSurfer version 4.5.0. I don't see any optional flagged arguments in which i can specify the version i am working with (the default version is 5.1.). I will be grate

[Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all

Hi, As of version 5.1 the Talairach stage precedes the nu-correction stage. Is there an option or possibility to switch this order? Cheers, Ed ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/f