[Freesurfer] Pial Surface, total area?

Hi FS Experts I want to get the total area from pia cortex, in order to normalize the parcellations measure. In lh.aparc.statsfile on there is a line: # Measure Cortex, WhiteSurfArea, White Surface Total Area, ** mm^2 > I've looking for this topic in the lista and I found there is a way to

[Freesurfer] wm-hypointensities label on MS subjects

Hi FS Experts: I've been using T1 data from MS subjects in order to try to identify lesion volume using wm-hypointensities label from aseg. I wonder if there is any tool which uses T2-flair sequence to the same goal? I'll be grateful if you can help Being all for now, I await a reply Guido

[Freesurfer] Which is the best volume to use to get intensity statistics?

Hi FS Expert I have just looked for this subject a long the list but I haven't found anything about. I have been working with FreeSurfer and I could get some segmentation from my T1 data. I used 'mri_segstats' to quantify volume of some subcortical region. Also I want to get intensity statistics

[Freesurfer] Get white and pial surfaces without using aseg.mgz

Hi FS Experts I'm using FreeSurfer to process my T1 data in order to get white and pial surfaces from it. I have a questions about usages of this file 'aseg.mgz'. In the 'recon-all' pipeline, there are some steps in which I can use it or don't use it depend on if I want or don't. I wonder What

Re: [Freesurfer] Skullstripping leaves a little bit of dura

ed fashion, but then you won't know for sure if > the results you found were due to an algorithmic artifact or the real > biology > > sorry > Bruce > > On Thu, 19 Nov 2015, Guido Orlando Pascariello wrote: > > Bruce, thanks for your reply >> >> My goal about cort

Re: [Freesurfer] Skullstripping leaves a little bit of dura

stripping don't matter > *unless* they mess up the surfaces in the vicinity (e.g. by being included > in the pial surface or creating topological defects that are incorrectly > fixed). > > cheers > Bruce > > > On Thu, 19 Nov 2015, Guido Orlando Pascariello wrote: > > H

[Freesurfer] Skullstripping leaves a little bit of dura

Hi Experts I'm using Freesurfer to quantify some subcortical volumes and cortical areas. I have been preprocessing my data using 'recon-all autorecon1' I have a question About Skullstripping. It is leaving a little bit of dura behind the head. I found '-gcut' which is useful to solve it but it

[Freesurfer] 'mri_normalize' & 'mri_nu_correct', how do they work?

Hi FS Experts I'm bioengineering student and I'm working on my final project to get my degree. it's about process neuroimaging (IRM) in order to cuantific some parameter which could be helpful for medicine (clinical neurology). I'm using FreeSurfer to process my data. It works realy good. But it