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
- segment all your subjects with the hippocampal module,
- register the subjects to MNI,
- Deform the hippocampal/amygdala segmentations
- 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 http://www.jeiglesias.com
On May 20, 2021, at 01:36, Hua, Jessica <Jessica.Hua@ucsf.edu mailto: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,
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