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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