Re: [Freesurfer] R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt

Do you mean to use them as seeds in FSFAST? You'll need to map them into the conformed space using mri_label2vol with the --regheader option (see the --help); view the volume to make sure it looks ok. Then run fcseed-config specifying the volume with -seg and the code with segid

On 02/06/2017 04:27 PM, stdp82@virgilio.it wrote:

Thank you very much. Could you provide me any suggestion to extract CA1 left or CA1 right? And how can I use them in FAST? By codes? Regards, Stefano

----Messaggio originale----
Da: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Data: 6-feb-2017 17.42
A: "stdp82@virgilio.it"<stdp82@virgilio.it>, "Freesurfer support
list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re: Hipposubfields in FreeSuerferColorLUT.txt

You would extract CA1 left from lh.hippoSfLabels-T1.v10.mgz and
CA1 right from rh.hippoSfLabels-T1.v10.mgz (assuming you’ve used
T1s to segment the subfields).
Cheers,
/E

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

...

On 6 Feb 2017, at 16:17, stdp82@virgilio.it
<mailto:stdp82@virgilio.it> wrote:

    Thanks Eugenio for your response.
    My apologies but this matter is unclear to me.
    If I would use results for FS-FAST how I can identify for
    example CA1 right from CA1 left?
    Additionally, for enthorinal which is the correct code in FAST?
    Stefano

        ----Messaggio originale----
        Da: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk
        <mailto:e.iglesias@ucl.ac.uk>>
        Data: 6-feb-2017 15.54
        A: "stdp82@virgilio.it
        <mailto:stdp82@virgilio.it>"<stdp82@virgilio.it
        <mailto:stdp82@virgilio.it>>, "Freesurfer support
        list"<freesurfer@nmr.mgh.harvard.edu
        <mailto:freesurfer@nmr.mgh.harvard.edu>>
        Ogg: Re: [Freesurfer] Hipposubfields in
        FreeSuerferColorLUT.txt

        Ciao Stefano,
        The results for the left and right hippocampi are in
        different files, so there’s no ambiguity despite the fact
        that they indeed share the same label codes.
        Cheers,
        /Eugenio

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

...

        On 6 Feb 2017, at 13:18, stdp82@virgilio.it
        <mailto:stdp82@virgilio.it> wrote:

        Hi list,
        within FreeSuerferColorLUT.txt, do the numbers between
        200-226 descrived the hippo-subfield outputs?
        Additionally, how can I obtain separate right and left
        masks?
        Thanks
        Stefano
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