External Email - Use Caution
Dear K
1. No 2. No, just the subject name; the subjects directory is specified separately. 3. Points at a file. 4. Yes. Cheers, /E
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Freesurfer schummanr@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 11 December 2018 at 15:24 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] segmentHA_T2 newbie questions
External Email - Use Caution Hi,
Trying to run the HippoAmig segmentation with T1-w and T2-w files for the first time and I have a few basic questions I could not resolve looking on the FS wiki:
1. Does the T2-w image need to be first recon-all processed like the T1-w?
On the wiki the command line is:
segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1
2. Does “bert” correspond to the directory for recon-all subject “bert” after been processed?
3. Does the FILE_ADDITIONAL_SCAN need to be a nit scan or should it point to the freesurfer directory post recon-all (this is kind of related to question #1 I realize).
4. In ANALYSIS_IS can I type just “T2”?
Thanks!
K