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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