Hi Eugenio,

just to confirm I understand the currently available options. There are two multispectral strategies (MPRAGE + high res 2D T2, or MPRAGE + 3D FLAIR). It would be great to see if the combo option improves things even further for the subfields (MPRAGE + high res 2D T2 + 3D FLAIR). Is that option at all possible with the available FS version or in the works?

Best,

    Jorge

On 05/09/2016 16:13, Iglesias, Eugenio wrote:

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.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

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