Worked! Thank you so much. Really appreciate the prompt response.
Best,
Priyanka
On Wed, Jul 29, 2015 at 11:34 AM, Eugenio Iglesias <e.igles...@bcbl.eu>
wrote:
> Hi again,
> instead of:
> mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
> your can run:
> mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
> Cheers,
> /E
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
> ----- Original Message -----
> From: "Priyanka Mehta" <priyankamehta0...@gmail.com>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Wednesday, July 29, 2015 11:26:04 AM
> Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
>
>
>
>
>
>
>
> Thanks Eugenio! Thats worked!
> One more question- how would I convert the lh.CA1.mgz that I get from the
> previous step to .nii format?
>
> Best,
> Priyanka
>
>
>
> On Wed, Jul 29, 2015 at 3:52 AM, Eugenio Iglesias < e.igles...@bcbl.eu >
> wrote:
>
>
> Hi Priyanka,
>
> you can use mri_extract_label for that. For example, if you are interested
> in CA1 (label 206), you can run:
>
> mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.mgz
>
> Cheers,
>
> Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
>
>
>
> ----- Original Message -----
> From: "Priyanka" < priyankamehta0...@gmail.com >
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Wednesday, July 29, 2015 7:59:37 AM
> Subject: [Freesurfer] FreeSurfer 6.0 dev version Output
>
> Hi,
>
> I am new to FreeSurfer and need help with hippocampal segmentation in the
> 6.0 dev version.
> I used the following command: recon-all -i ${subject}.nii -subject
> ${subject} -all -hippocampal-subfields-T1.
> I can also view the segmented hippocampal regions using the command:
> freeview -v nu.mgz -v lh.hippoSfLabels-T1.v10.mgz:colormap=lut -v
> rh.hippoSfLabels-T1.v10.mgz:colormap=lut.
>
> However, is there a way I can get a separate .nii file for each of my
> hippocampal subregion?
>
> I would really appreciate any help in the matter.
>
> Best,
> Priyanka Mehta
>
>
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