Hi Gonzalo,

the ii) and iii) produce directories that look like this: <tp1id>.long.<templateid> and <tp2id>.long.<templateid> These two directories are full subject-directories for time point 1 and time point 2. So if you are familiar with the cross sectional freesurfer subjects directory structure, you can find all kinds of information in there. For example in those you'll fine a stats/aseg.stats file containing the volumes of several subcotrical structures. You can compare these volumes between your 2 time points.

Note that a single patient is not very representative and you can probably not conclude much from it.

Best, Martin

On Mon, 2011-03-07 at 15:00 -0300, Gonzalo Rojas Costa wrote:

Hi Martin:

I processed a patient (with two MRIs in different dates) using the instructions in the web page that you told me, but I didn't understand very well the results that I got...

Which values I got in aseg.stats with:

i) recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -all

ii) recon-all -long <tp1id> <templateid> -all

iii) recon-all -long <tp2id> <templateid> -all

Sincerely,

Gonzalo Rojas Costa

El 03-03-2011 13:03, Martin Reuter escribió:

...

Hi Gonzalo,

you should run your data with the longitudinal stream (if you use fs 5.0 update mri_robust_template and recon-all first), see infos on : http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing

After processing, you can compare the volume measures in the /stats/aseg.stats files from the longitudinal directories. You can also map both the asegs from the long dirs to base and compute dice coefficients on specific labels, or you can compare surface measures etc. For all this you should be familiar with the cross sectional stream in freesurfer.

Best, Martin