Hi All,

I am new and a very basic question about freesurfer processing.

I ran recon-all on a high res-T1 image(128x128x80 matrix size), but after recon-all the folder mri contains resulted (brain.mgz and orig.mgz) T1 images has (127x128x128 matrix size).

1) how come the dimensions are changed? Is it normal?

2) how can i keep the dimensions same as the original?

3) is it possible that i will always get the higher matrix size image data?

for simplicity, i converted resulted orig.mgz to nii format and loaded it in to fslview. Please find the first image (Original) and the second image (after recon-all but orig.mgz).

Your help is greatly appreciated.

Kind regards,

Dhaval Shah

MRI Research fellow,MRI Physicist,Clinical Trial Research Staff
Buffalo Neuroimaging Analysis Center
State University of New York at Buffalo
Department of Neurology
100 High St., D-2, Buffalo, NY 14203
dshah@bnac.net//http://mbl.bnac.net