You could also run recon-all on the mni152 template, then run the hippo/amyg seg on the output. It will give you the same bad segmentation:)

On 5/20/2021 9:21 AM, Iglesias Gonzalez, Juan E. wrote:

Hi Jessica,

There’s no direct way of doing this, since the atlas lives it its own space and there’s no intensity volume you can deform to MNI, only probabilities.

Having said that, you could

1. segment all your subjects with the hippocampal module,

2. register the subjects to MNI,

3. Deform the hippocampal/amygdala segmentations

4. Average the segmentations in MNI space to get your ROIs in atlas space.

Cheers,

/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On May 20, 2021, at 01:36, Hua, Jessica <Jessica.Hua@ucsf.edu> wrote:

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Dear FreeSurfer experts,

I am trying to create a hippocampus ROI in FSL (MNI 152_2mm brain space) from the FreeSurfer 7.0 hippocampal/amygdala segmentation. How do I create this ROI?

Best,

Jessica
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