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

 

http://www.jeiglesias.com

 

 

 

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