Reposting my question:
This happens for all the segments that I've tried to extract using
mri_extract_label. They all show up as 128 nerve after mri_extract_label.
Is this a bug in the dev version?
Any help is greatly appreciated!
On Thu, Aug 20, 2015 at 3:45 PM, Priyanka <priyankamehta0...@gmail.com>
wrote:
> This happens for all the segments that I've tried to extract using
> mri_extract_label. They all show up as 128 nerve after mri_extract_label.
> Is this a bug in the dev version?
>
>
> > On Aug 20, 2015, at 3:20 PM, Lee Tirrell <ltirr...@nmr.mgh.harvard.edu>
> wrote:
> >
> > It seems that the command:
> >
> > mri_extract_label lh.hippoSfLabels-T1.v10.mgz 206 lh.CA1.nii
> >
> > put a value of 128 in lh.CA1.nii for the voxels labeled as 206 in
> lh.hippoSfLabels-T1.v10.mgz. You can run:
> >
> > mri_binarize --replace 128 206 --i lh.CA1.nii --o lh.CA1.nii
> >
> > and then the correct label names from the Lookup Table will show up.
> >
> > Best,
> > Lee
> >
> >> On Thu, 20 Aug 2015, Priyanka Mehta wrote:
> >>
> >> 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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