Hi Bruce
Sure, Its 170x256x256 axial
Truly,
Indika Walimuni
Research Associate
University of Texas Health Science Center
Houston, TX.
________________________________________
From: Bruce Fischl [[email protected]]
Sent: Thursday, April 01, 2010 1:45 PM
To: Walimuni, Indika S
Subject: RE: [Freesurfer] Volume masks
Hi Indika,
can you post these to the list so others can answer? What is the "native"
space you are using?
Bruce
On Thu, 1 Apr 2010, Walimuni, Indika S wrote:
> Hi Bruce
> Thanks for the reply. I used wmparc.mgz file for all the
cortical and sub-cortical WM/GM masks. This was the command, mri_binarize
--i wmparc.mgz --match "index from LUT" --o outputfile. This effect becomes
even more significant after I register the mask to like DTI/FA. But I don't
think it is a FreeSufer issue. I think I may have judged based on that. The
masks seems fine in the FreeSurfer space and the masks are OK. But when I
convert them to our native space using "mri_convert" I see a broadening
around the edges. I just want to test if there is another way and see the
difference. Am I using the wrong file? If I am to use aparc+aseg.mgz file
can I use it for all cortical, subcortical, WM and GM masks?
> Truly,
> Indika Walimuni
> Research Associate
> University of Texas Health Science Center
> Houston, TX.
> ________________________________________
> From: Bruce Fischl [[email protected]]
> Sent: Thursday, April 01, 2010 11:38 AM
> To: Walimuni, Indika S
> Cc: [email protected]
> Subject: Re: [Freesurfer] Volume masks
>
> Hi Indika,
>
> you should be able to do this using the aparc+aseg.mgz volume and
> mri_binarize. What command line did you use and can you give us an example
> of the "spilling"?
>
> cheers,
> Bruce
>
>
> On Thu, 1 Apr 2010,
> Walimuni, Indika S wrote:
>
>> Hi FreeSurfer List
>> Is their any way that I can generate cortical
> and sub-cortical volume masks by using the surfaces generated by
> FreeSurfer. If I can could anyone give me the proper command. Apparently,
> The masks I already generated using mri_binarize command, are little bigger
> and spilling into the surrounding.
>> Thank you in advance,
>> Truly,
>> Indika Walimuni
>> Research Associate
>> University of Texas Health Science Center
>> Houston, TX.
>> _______________________________________________
>> Freesurfer mailing list
>> [email protected]
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>
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