Dear Dhaval, when your recon-all finishs the process you will get images 256^3 and 1mm isootropic. The you can simply follow the instructions mentioned here https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat to send your images back to native space.
All the best, John
On Mon, Apr 3, 2017 at 4:35 PM, Dhaval Shah dshah@bnac.net wrote: 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).
- how come the dimensions are changed? Is it normal?
- how can i keep the dimensions same as the original?
- 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 [MailScanner has detected a possible fraud attempt from "dshah@bnac.net" claiming to be MailScanner has detected a possible fraud attempt from "dshah@bnac.net" claiming to be dshah@bnac.net//http://mbl.bnac.net%5D(http://dshah@bnac.net/http:/mbl.bnac.net)
-- 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 [MailScanner has detected a possible fraud attempt from "dshah@bnac.net" claiming to be MailScanner has detected a possible fraud attempt from "dshah@bnac.net" claiming to be dshah@bnac.net//http://mbl.bnac.net%5D(http://dshah@bnac.net/http:/mbl.bnac.net)
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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