Dear list and Eugenio, 

I have run for each subject

mri_label2vol --label SUBJ/label/rh.perirhinal_exvivo.thresh.label --regheader SUBJ/mri/norm.mgz --fill-ribbon --subject SUBJ --hemi rh --o SUBJ/mri/rh.perirhinal.nii.gz

next, to use FS-FAST on perihrinal.nii.gz, I have run

fcseed-config -seg SUBJ/mri/lh.perirhinal.nii.gz -fcname L_Perirhinal.dat -fsd rest -mean -cfg mean.L_Perirhinal.config

This error occurs:

ERROR: no segmentations IDs (-segid) or ROI (-roi) specified

What's should I do?

Thanks

Stefano

On Mon, 06 Feb 2017 13:59:38 -0800

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

----Messaggio originale----
Da: stdp82@virgilio.it
Data: 6-feb-2017 22.27
A: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: [Freesurfer] R: Re: R: Re: Hipposubfields in FreeSuerferColorLUT.txt

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 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>
Data: 6-feb-2017 15.54
A: "stdp82@virgilio.it"<stdp82@virgilio.it>, "Freesurfer support list"<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://cmictig.cs.ucl.ac.uk/

On 6 Feb 2017, at 13:18, 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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