Hi Erik, You can runsegmentHA_T2.sh on your FS processed subjects. You don’t need to run segmentHA_T1.sh first. The choice is whether you want to use T1+FLAIR (USE_T1=1) or only FLAIR (USE_T1=0). This command will generate outputs for both hippocampus and amygdala. The output will include multiple segmentations at different hierarchies, but only one text file with all the volumes. Regarding your old 6.0 measures: they’re safe because they used the suffix v10, and the new ones use the suffix v20 Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohan...@rcsi.ie> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Friday, 8 December 2017 at 14:15 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] new Amygdala and Hippocampus segmentation Hi FS experts, I have run an analysis using v6.0 and included the hippocampal subfields in the command using combined T1 and Flair segmentation. I would now like to look at the Amygdala segementation as described on the FS wiki. I would like to once again use both by T1 and FLAIR images but am a little confused about how to do that. Does the new tool haev to be run for T1 images and then followed by a second T2 specific run? for example would the following generate the hippocampus and amygdala meassures and generate a txt file for each hierarchy (ie HBT.txt, FS60.txt and CA.txt for hippoSF and amygNuc) ? segmentHA_T2.sh subject001 subject001_Flair.nni.gz T1andFlair USE_T1 /subject001 Will this overwrite any of my FS6.0 subfield measures present in the subject MRI dir? Thanks for any help you can provide . Erik Erik O'Hanlon Postdoctoral researcher [cid:image001.png@01D37030.F38C36B0] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie<http://www.rcsi.ie/> RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
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