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.