Workbench does not transform the GIFTI Surface Files.  Workbench draws volumes 
in coordinate space (not voxel IJK space) using the NIFTI ‘sform’ or ‘qform’.  
If the software you are using ignores the NIFTI  ‘sform’ or ‘qform’ that may be 
why the data does not align.

‘wb_command -file-information  <filename>’ will list the coordinate range for 
both a GIFTI surface file and a NIFTI volume file.


> On Apr 12, 2018, at 9:59 AM, Olivier Commowick <> 
> 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:
> Web:
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