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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