Thanks Bruce. Just wanted to make sure I've got the correct output.
Really appreciate the help.
Thanks again,
Priyanka Mehta
> On Aug 25, 2015, at 4:44 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote:
>
> Hi Priyanka
>
> that is what mri_extract_label is designed to do. This facilitates making
> density maps in a common space. If you want to get the original label # back
> you can use something like:
>
> mri_binarize --match 128 --binval <output label #> or something like that
>
> cheers
> Bruce
>
>
>> On Tue, 25 Aug 2015, Priyanka Mehta wrote:
>>
>> 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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