[Freesurfer] acquisition in 1 session vs 2 sessions

2013-11-09 Thread Daniel Ferreira
Dear experts, We are designing a study including a long MR protocol: 1) Localizer 2) Cal 3) T1-FSPGR 4) FLAIR 3D 5) DTI 1 6) DTI 2 7) fMRI Due to patients characteristics we were thinking on splitting the acquisition in two different sessions (session 1: sequences 1, 2, 3, 4; session 2: sequence

Re: [Freesurfer] acquisition in 1 session vs 2 sessions

2013-11-09 Thread Douglas Greve
I think the only thing you would have to worry about is the fMRI since the way the subject reacts to the task (or state of subject during rest) might change depending upon how long he/she has been in the scanner. Why not do the fMRI at #3? Then each population would be in the scanner for the

[Freesurfer] Modifying cortical surface for large dysplasia

2013-11-09 Thread Jonathan DuBois
Hi All, I have run recon-all on a subject with a large cortical dysplasia, and while the segmentation (aseg) seems to be relatively correct, there is a large region of dysplasia not included by the pail surface. The normalized intensity values for the cortex and the excluded region are very simila

[Freesurfer] Etiv difference in difference in same patient

2013-11-09 Thread Salil Soman
Hi, My understanding of etiv is that it is derived from the registration of a brain to atlas space and not actually derived from the freesurfer segmentation. I have a set of patients imaged at 2 time points that all have different etiv values between the first and second scan that are statistica