It depends on how graceful you want to be with resolving the overlap.
One simple way would be the following:
1. Change the binary values in B.mgz to 2 and C.mgz to 3 (A.mgz is
already 1). This can be done with mri_binarize
2. mri_concat A.mgz B.mgz C.mgz --max-index --o D.mgz
D.mgz will have a value of 1 where A=1 but not B or C
a value of 2 where B=1 but not C (regardless
of A)
a value of 3 where C=1 (regardless of A and B)
This allows you to set some priority between A, B, and C
3. You can then re-binarize to get three new masks
You can probably accomplish the same kind of thing with mri_mask as
Bruce suggests.
doug
On 6/6/12 2:00 PM, Bruce Fischl wrote:
> or use mri_mask. Or binarize to 2,4,8 etc.. them and add them, then replace
> the unique overlap values with something else
>
>
> On Wed, 6
> Jun 2012, Joshua Lee wrote:
>
>> Well you could mri_binarize the three volumes, then subtract regions
>> using fslmaths from the FSL suite. Of course this would create gaps
>> between your formerly adjacent regions.
>>
>>
>> Joshua
>>
>>
>> -
>> Joshua Lee
>> Graduate Student
>> Center for Mind and Brain&
>> Department of Psychology
>> University of California, Davis
>>
>>
>>
>> On Tue, Jun 5, 2012 at 11:46 PM, Yuko Yotsumoto<yuk...@gmail.com> wrote:
>>> Hello,
>>>
>>> With FreeSurfer v4.5, I have three functionally localized surface labels
>>> (A.label, B.label, C.label), and converted this label to volume by using
>>> mri_label2vol with --proj. I now have three volume labels, A.mgz, B.mgz,
>>> and C.mgz.
>>>
>>> Because these three labels are adjacent to each other, [A.mgz and B.mgz]
>>> and [B.mgz and C.mgz] share many voxels, and [A.mgz and C.mgz] also share a
>>> small number of voxels, while there is no overlap in the surface labels.
>>>
>>> I'd like to make these volume labels independent by somehow creating
>>> boundary into the volume so that each volume labels never share any voxels.
>>> What would be the best way to do so? Is there anything I can do using a
>>> command line?
>>>
>>> Best,
>>> Yuko Yotsumoto
>>>
>>>
>>>
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