[Freesurfer] area, and other dependent measures

2012-05-21 Thread Mahinda Yogarajah
Dear Experts, I have some related questions: 1) Am I right in thinking that the default settings for recon-all produce aparc files where the areas are based on white matter and not pia ? 2) Therefore am I right in assuming that when I use aparcstats2table across my subjects using "--meas area", t

Re: [Freesurfer] area, and other dependent measures

2012-05-22 Thread Mahinda Yogarajah
Hi, Sorry to re-post but I wanted to amend my questions on the basis of further reading I have done in the forum. Ignore questions 1 to 3. Instead 4) In a vertex wise analysis of area (using newer version of mris_preproc) what nuisance factors are people using - does it make sense to use t

Re: [Freesurfer] area, and other dependent measures

2012-05-22 Thread Douglas N Greve
On 05/22/2012 04:18 PM, Mahinda Yogarajah wrote: > Hi, > > Sorry to re-post but I wanted to amend my questions on the basis of > further reading I have done in the forum. Ignore questions 1 to 3. > > Instead > > 4) In a vertex wise analysis of area (using newer version of > mris_preproc)

Re: [Freesurfer] area, and other dependent measures

2012-05-22 Thread Bruce Fischl
intensity.deep and superficial are estimates of the intensity of the bottom of the cortex (deep) and the top of the cortex (superficial). These aren't generated by default, although we do have some tools for doing so. cheers Bruce On Tue, 22 May 2012, Douglas N Greve wrote: > > > On 05/22/2012