Hi Gunjan, if what you're trying to do is to bring brainmask.mgz to the native voxel space of your input scan, you can run mri_convert brainmask.mgz brainmaskResampled.nii.gz -rl input.nii.gz where input.nii.gz is the scan you fed to FreeSurfer's recon-all (e.g., recon-all -i input.nii.gz -s .... ) Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer ----- Original Message ----- From: "Gunjan Gautam" <gunjan.gemin...@gmail.com> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, December 1, 2014 2:23:12 PM Subject: [Freesurfer] Number of slices generated in the brainmask.mgz Hi FreeSurfers, brainmask.mgz is generating 256 slides per volume. How can I have control over it, in terms of generating less number of slides (say 181) per volume? Gunjan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
