Hi Priyanka,
in the mri directory of each subject, you will find a file named:
[lr]h.hippoSfLabels-<T1>-<analysisID>.v10.1mm.mgz
which stores the discrete segmentation volume in the 1 mm FreeSurfer voxel
space of that subject.
Kind regards,
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: Sunday, September 13, 2015 10:14:34 PM
Subject: Re: [Freesurfer] FreeSurfer 6.0 dev version Output
Hi again
I want to use my hippocampal segmentation for masking 2380 brain volumes. Is
there a way to find out using Freesurfer if the hippocampal subfields and the
2380 volumes are in the same space? The mean of the 2380 volumes and the
hippocampal subfields align correctly when I use Freesurfer's freeview to view
them. But does that also mean they are in the same voxel space?
And if they aren't in the same space, is there any way using Freesurfer that I
can have the two in the same space?
I really appreciate any suggestions!
Thanks,
Priyanka Mehta
On Tue, Aug 25, 2015 at 4:50 PM, Bruce Fischl < fis...@nmr.mgh.harvard.edu >
wrote:
of course
On Tue, 25 Aug 2015, Priyanka wrote:
> 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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>>> >>
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