<div dir="ltr">Hi Padraig,<div><br></div><div>The "direction" or "orientation" is the 3x3 portion of the 4x4 matrix, after dividing out the scale.</div><div><br></div><div>So if ITK is giving a direction like the following, it means that ITK allows the direction to include a mirror-flip (in this case, it's a flip along the z-axis):</div><div><br></div><div>1 0 0<br>0 1 0<br>0 0 -1</div><div><br></div><div>The vtkNIFTIImageReader doesn't allow a mirror flip in the QFormMatrix, so instead it re-orders the nifti slices in memory to undo the flip. When it does this, it also has to adjust the 4th column of the QFormMatrix since the 4th column now indicates the position of the last slice in the file, instead of the first slice in the file. The difference in position between the first slice and the last slice is (n - 1)*sz, where n is the number of slices and sz is the slice spacing. For your image, we can add (n - 1)*sz to -117.265 in order to get 30.149:</div><div><br></div><div> -117.265 + (52 - 1)*2.89048 = 30.149</div><div><br></div><div><div class="gmail_extra"><div class="gmail_extra">This accounts for the discrepancy.</div><div class="gmail_extra"><br></div><div class="gmail_extra"> - David</div><div class="gmail_extra"><br></div><div class="gmail_quote">On Sat, Nov 12, 2016 at 7:42 AM, padraig <span dir="ltr"><<a href="mailto:padraig.looney@gmail.com" target="_blank">padraig.looney@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF"><div><div class="gmail-h5">
<p>Hi David,</p>
<p><br>
</p>
<p>vtkNIFTIImageHeader (0x3346680)<br>
Debug: Off<br>
Modified Time: 85<br>
Reference Count: 1<br>
Registered Events: (none)<br>
DimInfo: 0x0<br>
Dim: 3 224 153 52 1 1 1 1 <br>
PixDim: -1 0.9195 1.40018 2.89048 0 0 0 0 <br>
VoxOffset:352<br>
IntentP1: 0<br>
IntentP2: 0<br>
IntentP3: 0<br>
IntentCode: 0<br>
DataType: 2<br>
BitPix: 8<br>
SliceStart: 0<br>
SclSlope: 1<br>
SclInter: 0<br>
SliceEnd: 0<br>
SliceCode: 0<br>
XYZTUnits: 0x2<br>
CalMax: 0<br>
CalMin: 0<br>
SliceDuration: 0<br>
TOffset: 0<br>
Descrip: ""<br>
AuxFile: ""<br>
QFormCode: 2<br>
SFormCode: 1<br>
QuaternB: 0<br>
QuaternC: 0<br>
QuaternD: 1<br>
QOffsetX: 102.536<br>
QOffsetY: 106.413<br>
QOffsetZ: 30.1491<br>
SRowX: -0.9195 0 -0 102.536<br>
SRowY: 0 -1.40018 -0 106.413<br>
SRowZ: 0 0 -2.89048 30.1491<br>
IntentName: ""<br>
Magic: "n+1"<br>
<br>
The direction in ITK is</p>
<p><br>
</p>
<p>1 0 0<br>
0 1 0<br>
0 0 -1<br>
</p>
I don't know how to see the direction in nibabel<br>
<br>
<br>
<div class="gmail-m_-5251641299272646700moz-cite-prefix">On 12/11/16 14:10, David Gobbi wrote:<br>
</div>
</div></div><div><div class="gmail-h5"><blockquote type="cite">
<div dir="ltr">
<div>
<div>Hi Padraig,</div>
<div><br>
</div>
<div>Can you show us the raw qform and sform fields from the
NIFTI header itself? In VTK, you can do this as follows:</div>
<div><br>
</div>
<div>>>> print(reader.GetNIFTIHeader())<br>
</div>
<div><br>
</div>
<div>The difference you see between nibabel, ITK, and VTK has
to do with differences in the way these packages deal with
the pixdim and the qfac of the nifti file. If you print the
Direction from the ITK image you might find that it differs
from nibabel, too.</div>
<div><br>
</div>
<div>For VTK, you can read all the gory details here:</div>
<div><br>
</div>
<div><a href="http://gitlab.kitware.com/vtk/vtk/blob/v7.0.0/IO/Image/vtkNIFTIImageReader.cxx#L738" target="_blank">http://gitlab.kitware.com/vtk/<wbr>vtk/blob/v7.0.0/IO/Image/<wbr>vtkNIFTIImageReader.cxx#L738</a></div>
</div>
<div><br>
</div>
<div> - David</div>
<div><br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sat, Nov 12, 2016 at 6:10 AM,
padraig <span dir="ltr"><<a href="mailto:padraig.looney@gmail.com" target="_blank">padraig.looney@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<div class="gmail-m_-5251641299272646700gmail-m_-103140333611607564moz-text-flowed" style="font-family:-moz-fixed;font-size:12px" lang="x-unicode">I have noticed some inconsistencies
in how NIFTI images are handled in VTK, ITK, and
NiBabel. ITK and NiBabel are in agreement with each
other and differ with VTK on the position of the
volume. The VTK output for a file is below. <br>
<br>
vtkNIFTIImageReader (0x1de67d0) <br>
Debug: Off <br>
Modified Time: 91 <br>
Reference Count: 2 <br>
Registered Events: (none) <br>
Executive: 0x1de7720 <br>
ErrorCode: Success <br>
Information: 0x1de6ad0 <br>
AbortExecute: Off <br>
Progress: 1 <br>
Progress Text: (None) <br>
FileName: /home/padraig/Desktop/59674/Se<wbr>eding/I0000003_59674_sn.nii
<br>
FileNames: 0 <br>
FilePrefix: (none) <br>
FilePattern: %s.%d <br>
FileNameSliceOffset: 0 <br>
FileNameSliceSpacing: 1 <br>
DataScalarType: unsigned char <br>
NumberOfScalarComponents: 1 <br>
File Dimensionality: 3 <br>
File Lower Left: On <br>
Swap Bytes: Off <br>
DataIncrements: (1, 1) <br>
DataExtent: (0, 223, 0, 152, 0, 51) <br>
DataSpacing: (0.9195, 1.40018, 2.89048) <br>
DataOrigin: (0, 0, 0) <br>
HeaderSize: 352 <br>
Internal File Name: (none) <br>
TimeAsVector: Off <br>
TimeDimension: 1 <br>
TimeSpacing: 1 <br>
RescaleSlope: 1 <br>
RescaleIntercept: 0 <br>
QFac: -1 <br>
QFormMatrix: -1 0 0 102.536 0 -1 0 106.413 0 0 1
-117.265 0 0 0 1 <br>
SFormMatrix: -1 0 -0 102.536 0 -1 -0 106.413 0 0 1
-117.265 0 0 0 1 <br>
NIFTIHeader: <br>
PlanarRGB: Off <br>
<br>
the qform given by nibabel is <br>
<br>
>>> ni_ob.get_qform() <br>
array([[ -0.91949999, 0. , 0. ,
102.53600311], <br>
[ 0. , -1.40017998, 0. ,
106.41300201], <br>
[ 0. , 0. , 2.89048004,
30.14909935], <br>
[ 0. , 0. , 0.
, 1. ]]) <br>
<br>
<br>
ITK has the origin at <br>
<br>
[-102.536, -106.413, 30.1491] <br>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
<br>
</div></div></div>
</blockquote></div><br></div></div></div>