Problems with mha_read_volume when reading MHA-File from Slicer3D

[Christian Richter]

Dear CERR community,

I have a problem with importing mha files (contours saved with Slicer3D).

For this task I wrote a small function (SlicerSS2CERR):

rois_header=mha_read_header(filelocation);

rois_volume = mha_read_volume(rois_header);

rois_zflipped = flipdim(rois_volume,3);

rois_zflipped_perm = permute(rois_zflipped,[2 1 3]);

planC=maskToCERRStructure(rois_zflipped_perm, 1, 1, SSname);

This code was working when I wrote it a few years ago. However, when I use it now, I get the following error:

Reference to non-existent field 'ElementNumberOfChannels'.

Error in mha_read_volume (line 79)

V = reshape(V,[str2num(info.ElementNumberOfChannels) info.Dimensions]);

Error in SlicerSS2CERR (line 9)

rois_volume = mha_read_volume(rois_header);

Indeed this field is not part of the header.. 

Filename: [1x107 char]

                   Format: 'MHA'

           CompressedData: 'true'

               ObjectType: 'image'

       NumberOfDimensions: 3

               BinaryData: 'true'

                ByteOrder: 'false'

       CompressedDataSize: 116764

          TransformMatrix: [1 0 0 0 1 0 0 0 1]

                   Offset: [-325 -325 -257.5000]

         CenterOfRotation: [0 0 0]

    AnatomicalOrientation: 'RAI'

          PixelDimensions: [1.2700 1.2700 2.5000]

               Dimensions: [512 512 168]

                 DataType: 'short'

                 DataFile: 'LOCAL'

                 BitDepth: 16

               HeaderSize: 344

Does anybody has an idea what could be wrong? Is there another way to read MHA files (Contours) from Slicer into CERR?

Best regards,

Christian

[ap...@mskcc.org]

Here is the script I use to import .mha structures that are deformed using Plastimatch. readmha.m is distributed along with CERR and it reads the ElementNumberOfChannels field. Hope this works for you.

 

[data3M,infoS] = readmha(structMhaFileName);

data3M = flipdim(permute(data3M,[2,1,3]),3);

isUniform = 1;

strName = ‘StructName’;

strCreationScanNum = 1;

planC = maskToCERRStructure(data3M,isUniform,strCreationScanNum,strName,planC);

 

Regards,

Aditya

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[Christian Richter]

Dear Aditya,

Thank you for your fast response. Unfortunately, when I tried your script, I got the following error message:

Error using reshape

To RESHAPE the number of elements must not change.

Error in readmha (line 119)

A = reshape(A,nchannels,sz(1),sz(2),sz(3));

A has 58382 elements (double). sz(1)=sz(2)=512, sz(3)=168, nchannels=1..

Do you have an idea what could be wrong?

Best regards,

Christian

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[ap...@mskcc.org]

Can you tell me what is the ElementType is  for your data? You can put a breakpoint on line 70 in readmha.m and print out the element_id variable.

Thanks,
Aditya

[Marta]

Hi Everyone,

I think Slicer3D uses compressed data Format for MHA volumes (you can look it up in the Header).

This cannot be read from matlab...

Can CERR read MHDs? These are uncompressed. Otherwise, I would suggest the following workflow:

1) save from Slicer3D in MHD Format (thus generating an mhd - header- and a raw data file)

2) Open up the mhd and raw files with text Editor.

3) modify in the mhd file the line Element Data File to say LOCAL (it should contain the Name of the raw data file at the beginning)

4) copy paste the Content of .raw file in a new line after the Element Data File line in the .mhd

5) save as .mha

This should work :)
my 2 cents

Marta

[Christian Richter]

Hi Marta and Aditya,

Thanks for your response. 

The data type is MET_SHORT

Hier is the header of the MHA:

ObjectType = Image

NDims = 3

BinaryData = True

BinaryDataByteOrderMSB = False

CompressedData = True

CompressedDataSize = 126812

TransformMatrix = 1 0 0 0 1 0 0 0 1

Offset = -325 -325 -297.3

CenterOfRotation = 0 0 0

AnatomicalOrientation = RAI

ElementSpacing = 1.27 1.27 2.50055

DimSize = 512 512 184

ElementType = MET_SHORT

ElementDataFile = LOCAL

@Marta: When I tried to export MHD from Slicer3D, it was also compressed (zraw). 

Also interesting to know: In the past I was able to import MHA into CERR with my routine. But somehow this has changed (new version on new computer, but also with the old CERR version it does not work any more)..so strange

[Marta Peroni]

Hi Christian,
as I thought, your data are compressed.
yes, also MHDs are compressed, but any uncompressing tool (e.g. winzip) should be able to unzip the raw.
Otherwise I suggest to use other type...
Marta