As I recently learned from messing with ANTS, ITK's coordinate system is
+x=left, +y=posterior, +z=superior, while the nifti coordinate system
(which workbench uses) is +x=right, +y=anterior, +z=superior.  This is the
reason for the negations on x and y.


On Fri, Apr 13, 2018 at 4:35 AM, Olivier Commowick <> wrote:

> Hi all and thanks for your answers,
> Just as a quick follow up I figured out how to align the vtk and images
> after conversion. The thing is I am using medinria that seems to read the
> nifti header differently (through the ITK reader) than workbench is.
> Basically, I have seen thanks to the wb_command -file-information and the
> hint on qform and sform that I had to apply a minus sign to all coordinates
> in the vtk files to have them aligned in medinria while it is not necessary
> in workbench.
> I am not exactly sur why this is happening but still it works now.
> Thanks a bunch
> Olivier
> On 12 Apr 2018, at 23:03, Timothy Coalson <> wrote:
> Workbench does not apply any additional transforms: the coordinates the
> file specifies are the ones it uses, directly (it actually ignores the
> affines in the gifti file, but writes an identity affine since gifti
> unfortunately requires at least one affine written there).  You can
> identify a vertex by clicking it or going to window->identify in wb_view,
> look at its coordinates in the information window, and then compare to the
> answer in matlab or other utilities to verify this and figure out if
> anything changes them.  You can also dump the coordinates to a metric file
> (.func.gii) with wb_command -surface-coordinates-to-metric .  We also use
> the sform/qform in nifti volumes as-is, so there shouldn't be any surprises
> there, either (as long as qform and sform match, which they will for
> volumes written from workbench - for fsl volumes, you may need to use a
> command to synchronize qform and sform).
> Freesurfer, unfortunately, has historically had a significant shift
> between its surface coordinates and voxel coordinates.  The HCP Pipelines
> fixed this so that the coordinates in the surfaces matched the voxel
> coordinates specified by the nifti header.  I think there is now an option
> in freesurfer that fixes these coordinates for you when converting to
> gifti, but I have no idea if it would apply when converting to vtk.
> As another option, caret5 supported some vtk formats, in addition to gifti
> and custom formats, so you could try that conversion.
> Tim
> On Thu, 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:
>> _______________________________________________
>> HCP-Users mailing list
> ---
> 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:
> _______________________________________________
> HCP-Users mailing list

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