Hi,
After applying the patch, we unfortunately had another issue with that file
from one of our customers.
The orient code of the header is 3 (flipped transverse), which was not handled
by the itkAnalyzeIO.
Applying the patch partially solved the issue, but the image is still flipped.
I noted a comment in itkAnalyzeDbh.h (I am using ITK 3.20).
It looks like orient codes 3, 4 and 5 are expected to have the middle axis
flipped since they use a different coordinate system as 0, 1 and 2 (left-handed
vs right handed).
I'd first like to confirm that behaviour.
I'd also like to have an idea of if/how easy or hard it would be to solve that
issue.
Thank you,
Mathieu
/**< The 'orient' field in the data_history structure specifies the primary
orientation of the data as it is stored
in the file on disk. This
usually corresponds to the orientation in
the plane of acquisition,
given that this would correspond to the
order in which the data is
written to disk by the scanner or other
software application.
It would be vary rare that you would ever
encounter any old ANALYZE 7.5
files that contain values of 'orient'
which indicate that the data has been
'flipped'. The 'flipped flag' values
were really only used internal to the
Analyze program to precondition data for
fast display in the Movie module,
where the images were actually flipped
vertically in order to accommodate
the raster paint order on older graphics
devices. The only cases you will
encounter will have values of 0, 1, or 2.
- hdr->orient "MayoClinic/Analyze"
Origin dims[1] dims[2] dims[3]
-
======================================================================
- 0 transverse-unflipped IRP
R->L P->A I->S
- 1 coronal-unflipped IRP
R->L I->S P->A
- 2 sagittal-unflipped IRP
P->A I->S R->L
- 3 transverse-flipped IRA
R->L A->P I->S
- 4 coronal-flipped SRP
R->L S->I P->A
- 5 sagittal-flipped ILP
P->A I->S L->R
- Where the Origin disignators are with
respect to the patient
- [(I)nferior|(S)uperior]
[(L}eft|(R)ight] [(A)nterior|(P)osterior]
SPECIAL NOTE: THE BEHAVIOR OF THIS IO
ROUTINE DIFFERS FROM THAT OF ANALYZE!
NO RE_ORIENTATION OF THE DATA WILL OCCUR
IN THE ITK IMPLEMENTATION.
Upon loading into the Analyze program,
all data is reoriented into the
3D Analyze Coordinate System.
The orientation of patient anatomy in the
3D Analyze Coordinate System
has a fixed orientation relative to each
of the orthogonal axes.
This coordinate system does fix the
origin in the subject's
Inferior-Right-Posterior location
relative to anatomy, with a
left-handed coordinate system for
specification of the other
anatomy relative to the axes as given
here:
- X-Y plane is Transverse
- X-Z plane is Coronal
- Y-Z plane is Sagittal
where:
- X axis runs from patient right (low X) to patient left (high X)
- Y axis runs from posterior (low Y) to anterior (high Y)
- Z axis runs from inferior (low Z) to superior (high Z)
On 2013-03-25, at 6:26 PM, Sean McBride <[email protected]> wrote:
> On Mon, 25 Mar 2013 22:05:45 +0000, Matt McCormick said:
>
>> After adding some missing colons :-)
>
> Whoops! I blame my coworker! :)
>
>> the patch has been pushed:
>>
>> http://itk.org/gitweb?p=ITK.git;a=c
>> ommit;h=a9fd63e26738f3c1449133c8077c67e072d1202a
>
> Thanks!
>
> --
> ____________________________________________________________
> Sean McBride, B. Eng [email protected]
> Rogue Research www.rogue-research.com
> Mac Software Developer Montréal, Québec, Canada
>
>
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