If you want the volume in the native space, then why not just register your volume to mni space, then map the label back to the individual? You could probably do that all with FSL (or SPM). BTW, the "volume" you get is not at all likely to be accurate. It will just reflect the registration in that area.

On 3/30/2021 4:28 PM, T. Pansuwan wrote:

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Dear Freesurfer experts,

As part of my project, I would need to have subthalamic nucleus as one of my ROIs in which this is not available by Freesurfer. I found a probabilistic subthalamic nucleus atlas in FSL atlases (in MNI152 space) and thought I would convert this to fsaverage space. I have attempted:

mri_label2vol —reg $FREESURFER_HOME/average/mni152.register.dat —seg STN-maxprob-thr25-0.5mm.nii.gz —temp $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz —o STN_mni152_in_mni305.nii.gz

But the location was much more dorsal than original,

1) I was wondering if there are alternative methods I should try and what could have been the problem?

At the end, I hope to obtain individual subject’s subthalamic nucleus volume,

2) I was wondering how to convert volume in fsaverage space to labels in fsaverage space so that I can convert the labels to native space?

Thank you so much!

Tanrada Pansuwan
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