Hi Eugenio
Thank you for the explanation, it makes sense to me now.
When I use Freeview to overlay my lh.CA1.nii on T1.nii, it aligns
correctly. However, when I view the segmentation with color map set to
Lookup Table and 'show existing labels only' checked, the lh.CA1.nii
segment shows as 128 Nerve label. Shouldn't it still be showing up as 206
CA1 label? I am confused.
On Wed, Aug 19, 2015 at 5:35 PM, Eugenio Iglesias <e.igles...@bcbl.eu>
wrote:
> Hi Prya,
> that is because MriCron is not that great at overlaying images that are in
> the same physical space but not in the same voxel space. You have two
> options here:
> 1. Use FreeSurfer's Freeview rather than MriCron to visualize the output.
> FreeView will correctly overlay the segmentation.
> 2. Use lh.hippoSfLabels-T1.v10.1mm.mgz (rather than
> lh.hippoSfLabels-T1.v10.mgz) when you call mri_extract_label. That volume
> lives in the same voxel space as T1.nii, and should be properly overlayed
> by MriCron. However, the resolution of the segmentation will be 1 mm,
> rather than the 0.333 mm that you'd get in option 1.
> 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 Mehta" <priyankamehta0...@gmail.com>
> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Sent: Wednesday, August 19, 2015 7:50:12 PM
> Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
>
>
>
> Hi
>
>
> This is a follow-up question to my previous problem.
> After I run recon-all -all -i ${subject}.nii -subject ${subject}
> -hippocampal-subfields-T1, I extracted the left CA1 using mri_extract_label
> lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii.
> I used MRICro to overlay this lh.CA1.nii on my T1.nii, however the
> alignment is not correct (see attached picture).
>
>
> I wonder what is causing this issue? Since the CA1 was extracted from the
> same T1 image, they should technically be in the same space and therefore
> should align correctly.
>
>
> Please advise.
>
>
> Thank you,
> Priyanka
>
>
> On Wed, Jul 29, 2015 at 11:37 AM, Priyanka Mehta <
> priyankamehta0...@gmail.com > wrote:
>
>
>
>
>
> 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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