Thank you Doug, I have found the summary file. So the final results that I have are the thickness data of the Mask.

What we wanted to find out was more how can we run the statistics not on the whole brain or one hemisphere, but only on one Mask (for i.e. a 3D Mask from FSL). the transformation of 3D to surface ?

Thank you for your help,
Alex.

Von: Doug Greve <greve@nmr.mgh.harvard.edu>
An: Alexandru Hanganu <hanganu.alexandru@yahoo.de>
CC: FS Mailing List <Freesurfer@nmr.mgh.harvard.edu>
Gesendet: Montag, den 8. Dezember 2008, 19:41:52 Uhr
Betreff: Re: [Freesurfer] Statistic analysing for a mask

what's your cmd? You need to make sure to add --in lh.thickness to get thickness in the summary file

Alexandru Hanganu wrote:

Thank you Nick, and Doug for your answers. I used both "--reshape" flag and "--noreshape" flag and the results after "mri_segstats" were in both cases:

    ..
    .
    .
    Voxel Volume is 1 mm^3
    Generating list of segmentation ids
    Found   2 segmentations
    Computing statistics for each segmentation
0     0   134504 134504
1     1   29338 29338

    Reporting on   2 segmentations

So I understand that these are the thickness data of the mask I used. Are these data in mm ? Because when using "mris_anatomical_stats" command line to see the thickness - the data is in mm, and is very different.

Sincerely,
Alex.
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