On 19 Sep 2016, at 14:13, pierre deman <deman.pierre@gmail.com> wrote:

Hi,

I have a short question about the additional T2 scan as well.

If I perform the full recon-all;

recon-all -s mySubject -i myT1.nii -T2 myT2.nii -T2pial -all -hippocampal-subfields-T1T2

do I still have to precise myT2scan.nii.gz T2 for using the t2 for the hippocampal subfields as well ? or it will automatically take the t2 precised for the t2pial ?

Cheers,

Pierre

On Mon, Sep 5, 2016 at 4:13 PM, Iglesias, Eugenio <e.iglesias@ucl.ac.uk> 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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