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

Dear Jorge,

In my case I am using either T1+T2 or T1+FLAIR. I had no intention of using all three at once, but now I am also wondering if this would be an improvement.

Cheers,

Renata

On Mon, Sep 5, 2016 at 4:54 PM, Jovicich, Jorge jorge.jovicich@unitn.it wrote:

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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