[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.
Re: [Freesurfer] Number of slices generated in the brainmask.mgz
Hi Gunjan you can't - all our volumes are 256 slices unless you are doing something unusual (which almost always means more slices, not less) cheers Bruce On Mon, 1 Dec 2014, Gunjan Gautam wrote: 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.
Re: [Freesurfer] Number of slices generated in the brainmask.mgz
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
Re: [Freesurfer] Number of slices generated in the brainmask.mgz
Thanks Eugenio, It worked. On Mon, Dec 1, 2014 at 7:11 PM, Eugenio Iglesias e.igles...@bcbl.eu wrote: 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 ___ 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.
