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I am working on project using Freesurfer’s “Segmentation of hippocampal subfields and nuclei of the amygdala” to segment the hippocampal subfields and compare it with a software called ASHS developed by the Penn Image Computing and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w SPC vNav.08 iso, ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to run the command: segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal sequence so to compare the two outputs, it would be ideal to also use the HighRes Hippocampal sequence. Please let me know if you need additional information. Thanks, Joshua E. Pasaye, B.S. (he/him/his) Clinical Research Coordinator | Imaging Core Mesulam Center for Cognitive Neurology and Alzheimer's Disease Northwestern University – Feinberg School of Medicine 300 E. Superior Street, Tarry 8-734, Chicago, IL 60611 (312) 503-5675 | joshua.pas...@northwestern.edu<mailto:joshua.pas...@northwestern.edu>
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