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.

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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