To all,
Connectome Workbench v. 0.83 has just been released and can be downloaded via http://www.humanconnectome.org/connectome/get-connectome-workbench.html
David VE
On Aug 21, 2013, at 10:25 AM, Matt Glasser <[log in to unmask]> wrote:
> Connectome Workbench command line tools (wb_command) can do this easily,
> e.g.
>
> wb_command -surface-apply-warpfield <in.surf.gii> <inversewarp.nii.gz>
> <out.surf.gii> -fnirt <forwardwarp.nii.gz>
>
>
> Importantly, when you are transforming surfaces/coordinates you have to
> use the inverse warpfield. The forward warp is only used for its NIFTI
> header info.
>
> Previously we had a hack that used FSL's img2stdcoord command, but that
> required stripping all the header info out of the surface file,
> transforming only the coordinates, and then adding it back in.
>
> Peace,
>
> Matt.
>
> On 8/21/13 5:18 AM, "Jesper Andersson" <[log in to unmask]>
> wrote:
>
>> Dear Keith,
>>
>> I'm afraid that we don't have a tool that lets you do this in a
>> straightforward manner. If you are reasonably familiar with C++
>> programming the tools/classes that fnirt are built upon lets you sample
>> the displacement fields in a continuous space (since they are represented
>> as splines it is technically not even interpolation) which is what you
>> need. But, it will involve getting your hand dirty with some C++.
>>
>> Jesper
>>
>> On 17 Aug 2013, at 19:59, Keith Jamison <[log in to unmask]>
>> wrote:
>>
>>> I have a number of surfaces from freesurfer and I want to warp them
>>> using a transform from FNIRT. There was a lot of manual editing of the
>>> surfaces, so I am hoping to not have to regenerate them from the warped
>>> surfaces. All of my attempts have run into problems working between
>>> coordinate systems.
>>>
>>> Is there a straightforward way to apply the FNIRT warp field to sets of
>>> X,Y,Z coordinates?
>>>
>>> Thanks,
>>> Keith
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