Hi Afsana,
I think adding "-odt int" or "-odt short" to your mri_convert command will set the data type of the output Nifti to int16, but I'm not sure if it conflicts with the -tr flag. You can also convert to .nii.gz instead of just .nii which will help keep the file size down.

Hope that helps,

Matt

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana [AAFZAL@mgh.harvard.edu]
Sent: Friday, April 22, 2016 11:52 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_convert doubling file size

Hi everyone,

I'm using mri_convert to reinforce TR information into the Nifti header in the following manner:

mri_convert $FILE $FILE -tr $TR

Before the conversion, my file size is usually around 550MB but after the conversion is doubles in size to ~1.1GB. In the Nifto file header I've noticed that the data type usually changes from int16 to float32.

Is there a quick way to decrease the file size or revert back to int16 without affecting the data?

Thanks for you help,

Afsana

______________________________

Afsana Afzal
Clinical Research Coordinator
Massachusetts General Hospital
Division of Neurotherapeutics
Department of Psychiatry: Neurosciences
149 13th St, Room 2612
Charlestown, MA 02129
Phone: 617-643-5129
Fax: 617-726-4078