Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

The same one; just change the input file and the analysis ID

- T2: recon-all -s mySubject -hippocampal-subfields-T1T2 myT2scan.nii.gz T2

- FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 myFLAIRscan.nii.gz FLAIR

Cheers,

/Eugenio

Juan Eugenio Iglesias Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata <rvp8@njit.edumailto:rvp8@njit.edu> wrote:

Dear FS experts,

I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0.

For controls on which I had already run recon-all -all, I added the T2 sequence with the following command:

recon-all -s <subject_name> \ -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID>

Now, if I want to do the same thing with FLAIR as the additional input, which flag should I use?

Thank you,

Renata