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Ahh, great! Thanks so much!
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@MGH.HARVARD.EDU>
Sent: 16 August 2022 08:58
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
 
It sets the output type to float and avoids rescaling of the intensities ;-)

Juan Eugenio Iglesias
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On Aug 15, 2022, at 18:45, Elizabeth Haris <e.haris@unsw.edu.au> wrote:

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That worked - thank you! 

If it's not too difficult, could you please tell me what that command does? (I had a quick google but couldn't find anything).

Thanks again!

Elizabeth
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@MGH.HARVARD.EDU>
Sent: 16 August 2022 08:29
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] transform amygdala mask from FS to native space
 
Uuumm can you please try adding “-odt float” to the command?


On Aug 15, 2022, at 18:23, Elizabeth Haris <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.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
 


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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