What tools are you using that require VTK?



On 4/12/18, 9:59 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Olivier Commowick" <hcp-users-boun...@humanconnectome.org on behalf of
olivier.commow...@inria.fr> wrote:

>Hi HCP users and moderators,
>I have been trying lately to convert the gifti files from the
>preprocessed data of HCP (in the Native folder) to the VTK format since
>there are tools we use that are relying solely on this format. I have
>been encountering problems though with the converted files that do not
>align properly with the image in visualization softwares. To start with,
>I have tested two conversion methods: one through matlab and SPM12, and
>one through the mris_convert tool of freesurfer, both with the default
>parameters (no info on the T1 image itself). In both cases, the result is
>the exact same i.e. a vtk surface that does not align with the T1 image
>(with at least two flips on the X and Y axes but probably not only).
>What is weird to me though is that the gifti and T1 image align perfectly
>in connectome workbench. This makes me think that either the software is
>doing something specific to align them or is accounting for something in
>the gifti file that I could not see. The only info I saw is that the
>gifti files are in Talairach space (NIFTI_XFORM_TALAIRACH) and no
>orientation matrix is given (identity).
>Would anyone know more about this ? Is workbench applying some
>transformation on the fly to the gifti files when loading (in which case
>which one would be helpful) ? Am I using the wrong files or am I missing
>something (and SPM and freesurfer too) in the gifti files from HCP ?
>Thanks a lot in advance
>Olivier Commowick, Ph.D.
>Research Scientist
>INRIA Rennes - Bretagne Atlantique, VISAGES Team
>Campus de Beaulieu
>35042 Rennes
>Phone: +33 2 99 84 25 92
>Email: olivier.commow...@inria.fr
>Web: http://olivier.commowick.org/
>HCP-Users mailing list

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