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Dear FreeSurfer Experts,
I am running my subjects through autorecon-1 and then the mri_segment_hypothalamic_subunits function to obtain the divisions of the hypothalamus. However, I just wanted to confirm whether the results are already corrected for intracranial volume during autorecon-1 or within the hypothalamic segmentation (as I assume they would be if I were to run obtain the aseg segmentation further along the pipeline?). Or do I need to calculate eTIV separately?
If so, how do you recommend going about this? Perhaps running something like mri_segstats --subject subjid --etiv-only?
Any help is appreciated. Thank you, Asmin
UCL Queen Square Institute of Neurology
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It is not corrected for eTIV. You can compute eTIV as you suggest, ie, running autorecon1 then running mri_segstats --xfm2etiv subject/mri/transforms/talairach.xfm etiv.dat
On 5/9/2023 8:01 AM, Asmin Alam wrote:
External Email - Use Caution
Dear FreeSurfer Experts,
I am running my subjects through autorecon-1 and then the mri_segment_hypothalamic_subunits function to obtain the divisions of the hypothalamus. However, I just wanted to confirm whether the results are already corrected for intracranial volume during autorecon-1 or within the hypothalamic segmentation (as I assume they would be if I were to run obtain the aseg segmentation further along the pipeline?). Or do I need to calculate eTIV separately?
If so, how do you recommend going about this? Perhaps running something like mri_segstats --subject subjid --etiv-only?
Any help is appreciated. Thank you, Asmin
UCL Queen Square Institute of Neurology
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Asmin Alam -
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