### Author:  [@mihail.isakov](https://discourse.itk.org/u/mihail.isakov)
#### Post date: [February 22, 2019, 9:14pm UTC](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612/4 "2019-02-22T21:14:20Z")
Honestly, i didn’t know where to do the step - in itk::GDCMImageIO
`void GDCMImageIO::Write(const void *buffer)`
works already with _void \* buffer_
and direction is taken [from metadata](https://github.com/InsightSoftwareConsortium/ITK/blob/73188f4e7b1bb558ed0f1871ac119c926950e49d/Modules/IO/GDCM/src/itkGDCMImageIO.cxx#L901)
`ExposeMetaData< DoubleMatrixType >( dict, key, directionMatrix );`
or already set, probably here is “too late”, i have to learn how IO factory works exactly 🤓 🤔
Thank you for reply
---
### Author:  [@mihail.isakov](https://discourse.itk.org/u/mihail.isakov)
#### Post date: [February 23, 2019, 8:25pm UTC](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612/5 "2019-02-23T20:25:22Z")
Looked at image IO.
IMHO, filter could be applied here
[itkImageFileWriter.hxx](https://github.com/InsightSoftwareConsortium/ITK/blob/73188f4e7b1bb558ed0f1871ac119c926950e49d/Modules/IO/ImageBase/include/itkImageFileWriter.hxx#L174)
_if IO is GDCM image IO_ (DCMTK too? never tried) and _if image dimension is 3_.
Changing of metadata is not required.
For justification (another one):
For DICOM file 6 values from direction matrix will be taken (x and y direction), because 3rd is defined in DICOM as right handed cross product. From GDCM IO:
```
// Do the direction now:
// if the meta dictionary contains the tag "0020 0037", use it
const bool hasIOP = ExposeMetaData(dict, "0020|0037",tempString);
if (hasIOP)
{
double directions[6];
sscanf(tempString.c_str(), "%lf\\%lf\\%lf\\%lf\\%lf\\%lf", &(directions[0]), &(directions[1]), &(directions[2]),&(directions[3]),&(directions[4]),&(directions[5]));
image.SetDirectionCosines(0, directions[0]);
image.SetDirectionCosines(1, directions[1]);
image.SetDirectionCosines(2, directions[2]);
image.SetDirectionCosines(3, directions[3]);
image.SetDirectionCosines(4, directions[4]);
image.SetDirectionCosines(5, directions[5]);
}
else
{
image.SetDirectionCosines(0, m_Direction[0][0]);
image.SetDirectionCosines(1, m_Direction[0][1]);
if ( m_Direction.size() == 3 )
{
image.SetDirectionCosines(2, m_Direction[0][2]);
}
else
{
image.SetDirectionCosines(2, 0);
}
image.SetDirectionCosines(3, m_Direction[1][0]);
image.SetDirectionCosines(4, m_Direction[1][1]);
if ( m_Direction.size() == 3 )
{
image.SetDirectionCosines(5, m_Direction[1][2]);
}
else
{
image.SetDirectionCosines(5, 0);
}
}
```
E.g. RAI and RAS:
1 0 0
0 1 0
0 0 1
and
1 0 0
0 1 0
0 0 -1
For both orientations, the same _Image Orientation Patient_ “1, 0, 0, 0, 1, 0” will be assumed and for multi-frame image GDCM will calculate wrong slice origins for RAS image.
Sincerely
---
### Author:  [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)
#### Post date: [February 24, 2019, 1:54am UTC](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612/6 "2019-02-24T01:54:43Z")
> [@mihail.isakov](#):
>
> _if IO is GDCM image IO_ (DCMTK too? never tried) and _if image dimension is 3_ .
It is tricky since _itkImageFileWriter.hxx_ cannot depend on _itkGDCMImageIO.h_ – _itkGDCMImageIO.h_ may not be available if the _ITKIOGDCM_ module is not enabled, and the _ITKIOImageBase_ module cannot depend on on the _ITKIOGDCM_ module (the reverse dependency exists).
In one approach, if DCMTK behaves the same, we could apply the fix for output files with the _.dcm_.
Or, we could apply the fix in _itkGDCMImageIO.cxx_, even though it is more difficult since the image has been decomposed.
---
### Author:  [@mihail.isakov](https://discourse.itk.org/u/mihail.isakov)
#### Post date: [February 24, 2019, 2:14am UTC](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612/7 "2019-02-24T02:14:03Z")
Oh, yes. Important to know, thank you.
I’ve just tried to add
std::cout \<\< m\_ImageIO-\>GetNameOfClass() \<\< std::endl;
at this point, line 174, before line with
`auto * nonConstInput = const_cast< InputImageType * >( input );`
seems _m\_ImageIO_ knows name of class, without including new headers.
Probably it is enough, i’ll try and report.
Sincerely
---
### Author:  [@mihail.isakov](https://discourse.itk.org/u/mihail.isakov)
#### Post date: [February 24, 2019, 8:12pm UTC](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612/8 "2019-02-24T20:12:02Z")
@matt.mccormick you are right, of course. ImageFileWriter is bad place, the problem is - some things happen in ::Write(), some in ::GenerateData(), always accessing image like
`const InputImageType *input = this->GetInput();`
and buffered region, streaming, pipeline, many possible issues. It is possible, but will require too many changes, not worth… Probably possible ways are either do the job in GDCM IO class, as you have suggested, also tricky, or just give a warning (or error). I shall play again little later… Thank you
---
### Author:  [@jond01](https://discourse.itk.org/u/jond01)
#### Post date: [April 16, 2020, 8:25pm UTC](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612/9 "2020-04-16T20:25:01Z")
Hi, is there any update with this?
Apparently, every dicom (single 3d image or dicom series) with a left-handed orientation (24 out of 48, e.g. RAS) is saved in a wrong way. I think that it is a serious bug, but couldn’t find one in the open issues.
I can provide a short python code which demonstrates the issue.
Maybe a solution will be to add a (-1) factor to the “_Spacing Between Slices_” tag for left-handed orientations?
---
### Author:  [@mihail.isakov](https://discourse.itk.org/u/mihail.isakov)
#### Post date: [April 16, 2020, 10:02pm UTC](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612/10 "2020-04-16T22:02:17Z")
i also think it is critical issue, actually best workaround, IMHO, is to apply change orientation filter for incompatible orientations (e.g. RAS to RAI) before exporting to multi-frame DICOM.
---
### Author:  [@jond01](https://discourse.itk.org/u/jond01)
#### Post date: [April 17, 2020, 11:40am UTC](https://discourse.itk.org/t/nifti-rpi-orientation-file-exported-to-dicom-wrong-orientation/1612/11 "2020-04-17T11:40:30Z")
Ok thank you. I just opened an issue in github:
>
>
> Description
> Out of 48 possible orientations for a 3d image, the 24 left-handed orientations are treated incorrectly when saving a multi-frame dicom...
You’re welcome to add your ideas 🙂