Uuumm can you please try adding “-odt float” to the command?
Juan Eugenio Iglesias http://www.jeiglesias.com
On Aug 15, 2022, at 18:23, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
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Hi Eugenio,
Yes, I did. This gives me a binary mask, which is why I was confused and at a loss as to what else I could to do. Any suggestions?
Thanks, Elizabeth
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@MGH.HARVARD.EDUmailto:JIGLESIASGONZALEZ@MGH.HARVARD.EDU> Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 16 August 2022 at 12:42 am To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
Dear Elizabeth, You command looks good to me. Did you visualize lh_Amyg_native.mgz with colormap=lookup table? Cheers, /Eugenio
Juan Eugenio Iglesias MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.comhttp://secure-web.cisco.com/1pwL3YVC95FMB_GHaFVaRq2LS-ak5rEvOAddlJRB07pe45WUvCSp05LF1S089h0oP4XCQ3hJcM65zQ0DhzpUOWBOjh1ImMeygYvNzIfrDxmcNE8rtljT6FQireC73u3qNT7_7SDo22lqWjYplhx738o8EFMp9Eh1Eysbxhi-IM6TyFuiqgYRF4v0q3mvcvtDY-CoGcquvDQQcrpDjJ4rsQNxqT05OQ-2KOd4ps1PjTDavvaZqV9-HseiCjsawlq63MBMmiTMtypIw-bHsCJ7v7ogTWw2MX82EsmO4ZI_OFZS5o34I084CVKgSvP_9FY-Z/http%3A%2F%2Fwww.jeiglesias.com
On Aug 14, 2022, at 18:58, Elizabeth Haris <e.haris@unsw.edu.aumailto:e.haris@unsw.edu.au> wrote:
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I have segmented hippocampal/amygdala masks for my participants with the segmentHA_T1.sh script, but I am wanting to transform these masks into native space for analysis. I have tried using mri_convert (command below), however, this command gives me a binary mask rather than one containing all the segments. Is there an additional step I need to include to retain the information from the segmented data when transforming the mask?
mri_convert -rl rawavg.mgz -rt nearest lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz ./lh_Amyg_native.mgz
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