thank you.
Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: sorry, on "any" surface configuration....
On Tue, 30 May 2006, Bruce Fischl
wrote:
> no, you should be able to overlay it on and surface configuration or patch
> from that hemisphere.
>
> Bruce
>
> On Tue, 30 May 2006, adam walczak wrote:
>
>> Thanks...that worked. I am also trying to create a flattened image to
>> overlay my ROI data on. Will I need to make a new overlay with the
>> flattened image as the surface template?
>>
>> Thanks.
>>
>> Adam
>>
>> Doug Greve wrote:
>> You can do it with tksurfer, as in:
>>
>> tksurfer subject lh inflated -overlay youroverlay.mgh
-overlay-reg
>> register.dat
>>
>> douyg
>>
>> adam walczak wrote: Thanks Doug...I was also wondering if it were possible
>> to load our own overlays on the surface (eg. pial surface)?
>>
>> Would this be done using tksurfer or would some other program/command be
>> needed?
>>
>> Thanks.
>>
>> Adam
>>
>> Doug Greve wrote:
>> I think I see what you mean. But the answer is no, FreeSurfer will always
>> resample to 256^3, 1mm, coronal. But you can still use your ROIs, you just
>> need to make a registration matrix first. Do this:
>>
>> tkregister2 --targ orig.mgz --mov rawavg.mgz --reg register.dat
>>
>> It is assumed that rawavg.mgz is in the native space (same
>>
>> This will bring up a window with a control
panel. Hit the Compare button.
>> The two images should be identical. Look at a few slices/orientations to
>> assure this. Hit the Save Reg button -- this creates register.dat
>>
>> Then run mri_vol2vol. I've recently modified it and you might not have the
>> most recent version, so I've copied it here:
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_vol2vol
>>
>> specify your roi volume as the --mov and use nearest neighbor interp
>>
>> doug
>>
>>
>>
>>
>> adam walczak wrote:
>> Doug,
>>
>> I think that you answered my question. We wanted to
>> overlay some ROI files onto the freesurfer created
>> surfaces, but the ROIs were made before we ran the
>> images through freesurfer. So we wanted to make sure
>> that we could keep the
surfaces in the same space as
>> the ROIs we
>> created...is that an answer to your
>> question?
>>
>> Adam
>>
>> --- Doug Greve wrote:
>>
>>
>>
>> What do you mean by "native space"? The
>> reconstruction is not done in
>> tal space.
>>
>> doug
>>
>> adam walczak wrote:
>>
>>
>>
>> Hello,
>>
>> I want to make cortical surface images that we
>>
>>
>> will overlay with our
>>
>>
>> own masks. But we want to do this in native
>>
>>
>> space. So, I was
>>
>>
>> wondering if it is possible to go thorugh the
>>
>>
>> reconstruction process
>>
>>
>> to make the
surfaces without ever using the
>>
>>
>> talairach transform and
>>
>>
>> keeping everything in its native space.
>>
>> Thank you,
>>
>> Adam
>>
>>
>> adam
>>
>>
>>
>>
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>>
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>>
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adam
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