Plastimatch convert

[Laura Panizzi]

Hi,

I'm trying to convert with plastimatch DICOM image in .mha format. I follow the instruction on the web site and it works, but with some images I've got wrong Origin, Spacing and Direction while the Size is right. Independently from the input image I get this values:

Origin = 0 0 0

Spacing = 1 1 1

Direction = 1 0 0 0 1 0 0 0 1

that seems to be default value.

I've open the same image with ImageJ and there the values are right (Origin = -120.48 -125.93 -4.7, Spacing = 0.89 0.89 3.4, Direction = 0.997 -0.03 0.06 0.06 0.91 -0.39 ).

Where is the problem?

Thanks,

Laura

[Paolo Zaffino]

Hi Laura,

which command are you using to convert the files?

Regards.

Paolo

---

Da: Laura Panizzi <laura....@gmail.com>
A: plast...@googlegroups.com
Inviato: Lunedì 15 Aprile 2013 12:26
Oggetto: [Plastimatch] Plastimatch convert

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[Laura Panizzi]

Hi Paolo,

I use this command:

plastimatch convert --input dicomDIR --output-img img.mha

It works with almost all the images.

thanks,

Laura

[Paolo Zaffino]

Hi,

I think the command is right.

Are you trying to convert a dicom dataset (# 2D img > 1) into a 3D mha file, right? 

What are the real geometrical information that you read from the dicom header?

So some image set have no problem, while other set are wrong...did I understand well?

Paolo

---

Da: Laura Panizzi <laura....@gmail.com>
A: plast...@googlegroups.com

Cc: Paolo Zaffino <p.za...@yahoo.it>
Inviato: Lunedì 15 Aprile 2013 12:34
Oggetto: Re: [Plastimatch] Plastimatch convert

[Laura Panizzi]

Yes, you understand well, I'm trying to convert dicom dataset into a 3D mha file.

The real geometrical information are:

0018,0088 Spacing Between Slices: 3.4

0020,0032 Image Position (Patient): -120.48 \ -125.93 \ -4.74

0020,0037 Image Orientation (Patient): 0.997 -0.038 0.066 0.061 0.917 -0.393 

0028,0030 Pixel Spacing: 0.898 0.898

while converting, in the command line I get instead:

Origin = 0 0 0

Spacing = 1 1 1

Direction = 1 0 0 0 1 0 0 0 1

This happen to me with two images, an anonymized PET and a dwi MR. 

I thought that could be the process of anonymizing the cause, but this time the image is not anonymized.

thanks,

Laura

[Sharp, Gregory C.]

It's possible there is a bug.  Could you share an (anonymized) image

that exhibits this problem?

---

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of Laura Panizzi
Sent: Monday, April 15, 2013 7:16 AM
To: plast...@googlegroups.com
Cc: Paolo Zaffino
Subject: Re: [Plastimatch] Plastimatch convert

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[Laura Panizzi]

Hi Gregory,

this is one anonymized image, in attachment.

Thanks,

Laura

[Sharp, Gregory C.]

Hi Laura,

 

Are you using dcmtk or gdcm build of plastimatch?

 

Greg

---

From: Laura Panizzi [mailto:laura....@gmail.com]
Sent: Monday, April 15, 2013 11:08 AM
To: plast...@googlegroups.com
Cc: Paolo Zaffino; Sharp, Gregory C.

[Laura Panizzi]

Hi Greg,

I'm using gdcm build (on Mac Os)...I've installed the one that was selected by default, because I'm new on Plastimatch and ITK and I don't know the difference.

Thanks,
Laura

[Sharp, Gregory C.]

Hi Laura,

 

Sorry, one more question, which version of ITK?

 

(The ITK 3 comes with gdcm v1, but ITK 4 comes with gdcm v2.)

 

Greg

---

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of Laura Panizzi

Sent: Tuesday, April 16, 2013 12:53 PM
To: plast...@googlegroups.com
Cc: 'Laura Panizzi'; Paolo Zaffino; Sharp, Gregory C.

[Laura Panizzi]

Hi Greg,

I have installed ITK 4.3.1.

Laura

[Sharp, Gregory C.]

Hi Laura,

 

OK.  Got it.  That is probably the problem. 

Unfortunately gdcm v2 is not supported.

 

Would you consider downgrading to ITK 3?

 

Another choice would be to re-build with dcmtk.

 

Greg

---

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of Laura Panizzi

Sent: Tuesday, April 16, 2013 1:49 PM

[Laura]

Hi Gregory,

First of all I'll try to re-build plastimatch with dcmtk, It seems to me the simplest way.

Then if it doesn't works yet I'll try to downgrade to ITK 3.

Thank you very much,

Laura

2013/4/16 Sharp, Gregory C. <GCS...@partners.org>

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[Laura Panizzi]

Hi Gregory,

finally I've installed ITK 3 and now it works!

thank you very much,

Laura

[Laura Panizzi]

Hi Gregory,

I'm still here...the new installation works via command line, but if I call plastimatch in Matlab, with the comman system('plastimatch convert --input --output-img') I get a wrong result.

With the same image, from command line I get:

The directory:

 .../Anonymous/CT

Contains the following DICOM Series:

 1.2.826.0.1.3680043.2.1322.2.6043718.36103110489.1.13.750000512512

Now reading series:

 1.2.826.0.1.3680043.2.1322.2.6043718.36103110489.1.13.750000512512

Setting PIH from M_IMG

PIH is:

Origin = -150 -150 -135.34

Size = 512 512 93

Spacing = 0.585938 0.585938 3.26999

Direction = 1 0 0 0 1 0 0 0 1

Rtds_warp: Saving m_img (ct.mha)

Trying to write image to ct.mha

Rtds_warp: warp and save ss.

Finished!

while, converting the same image in Matlab i get:

system('plastimatch convert --input .../Anonymous/CT --output-img ct.mha')

The directory: 

.../Anonymous/CT

Contains the following DICOM Series: 

1.2.826.0.1.3680043.2.1322.2.6043718.36103110489.1.13.750000512512

Now reading series: 

1.2.826.0.1.3680043.2.1322.2.6043718.36103110489.1.13.750000512512

Setting PIH from M_IMG

PIH is:

Origin = 0 0 0

Size = 0 0 93

Spacing = 1 1 1

Direction = 1 0 0 0 1 0 0 0 1

Rtds_warp: Saving m_img (ct.mha)

Trying to write image to ct.mha

ITK exception writing image file.

itk::ExceptionObject (0x101eb2f30)

Location: "void itk::ImageFileWriter<TInputImage>::Write() [with TInputImage = itk::Image<short int, 3u>]" 

File: /Users/lauracecypanizzi/Desktop/Topo/TesiMagistrale/InsightToolkit-3.20.1/Code/IO/itkImageFileWriter.txx

Line: 271

Description: itk::ERROR: ImageFileWriter(0x101eb1f00): Largest possible region does not fully contain requested paste IO regionPaste IO region: ImageIORegion (0x7fff5fbfe2d0)

  

Dimension: 3

Index: 0 0 0 

Size: 0 0 93 

Largest possible region: ImageRegion (0x7fff5fbfe390)

Dimension: 3

Index: [0, 0, 0] 

Size: [0, 0, 93]

Rtds_warp: warp and save ss.

Finished!

With the previous version of ITK/plastimatch I didn't have this problem.

Well, I did something in installation? Is It solvable or can I use plastimatch only from command line?

Thanks very much,

Laura