External Email - Use Caution 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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