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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.edu> on behalf of "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@MGH.HARVARD.EDU>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 16 August 2022 at 12:42 am
To: Freesurfer support list <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
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On Aug 14, 2022, at 18:58, Elizabeth Haris <e.haris@unsw.edu.au> wrote:

 

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Hi Freesurfer Developers,

 

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

 

Many thanks,

Elizabeth

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