Converting Nifti ROI to Dicom RTSTRUCT

[Sudhir Pathak]

Dear All,

I wanted to convert a nifti ROI file (.nii) to dicom RTSTRUCT. I tried to install plastimatch on three different machine (two with ubuntu 14.04 and one with 15.04 )  by compiling plastimatch with ITK4.5 and 3.20.2 and by installing plastimatch from UBUNTU repo. 

I am trying to use this command listed on documentation page:

plastimatch segment \
  --input water_dicom \
  --output-dicom water_dicom \
  --lower-threshold -500

But I don't see any commandline options corresponds to "--output-dicom water_dicom" in compiled or ubuntu repo version. I might be missing something.
Is there any other way to do this?


Thanks a lot,


Sudhir

[Paolo Zaffino]

Hi Sudhir,
I didn't understand what you want to do.
Do you need to convert a ROI stored in a nifti file into a dicomRT?

Best.
Paolo

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[Sudhir Pathak]

Thanks for reply. 

Yes. I have an anatomical ROI from T1 image (as nifti with 0 and 1 label) and wanted to convert to dicomrt RTSTRUCT.

Thanks,

Sudhir 

[Paolo Zaffino]

Hi Sudhir,
first of all you need to convert you T1 image (I guess it is a nifti file) into dicoms.
To do this, assuming that your T1 file is named "T1.nii.gz", run:
plastimatch convert --input T1.nii.gz --output-dicom T1_dicom

After that, assuming that your ROI files are stored into a folder named "ROIs" you can run:
plastimatch convert --input-prefix ROIs --interpolation nn --referenced-ct T1_dicom --output-dicom ROIs_dicom

and into the folder "ROIs_dicom" (created by plastimatch) you will find the dicomRT.

Let me know if it works.
Best.

Paolo

[Sudhir Pathak]

Hello Paolo,

I ran the command, but got an error in the last one: (ROIs contains one file thalamus_label49.nii, T1_dicom have 256 dicom files from first command)

Please let me know your thoughts. I really appreciate your time and help.

Thanks,

Sudhir

plastimatch convert --input-prefix ROIs --interpolation nn --referenced-ct T1_dicom --output-dicom ROIs_dicom

Loading RDD

Best chunck:

  Slices 0 to 255 from (0 to 255)

  Z_loc = 111.789825 111.789825

  Slice spacing = 0.000000

Samp_per_pix: 1

Phot_interp: MONOCHROME2

Bits_alloc: 16

Bits_stored: 16

High_bit: 15

Pixel_rep: 1

S/I = 1.000000/-1024.000000

Image looks ok.  Try to load.

Loading RDD complete

Setting PIH from RDD

PIH is:

Origin = -125.147 111.79 111.79

Size = 256 256 256

Spacing = 1 1 0

Direction = 1 0 0 0 -0 -1 0 1 -0

Rt_study_warp: Convert ss_img to cxt.

Rt_study_warp: Apply dicom_dir.

Rt_study_warp: Set geometry from PIH.

Rt_study_warp: Set rasterization geometry.

Segmentation fault

Sudhir

[Sharp, Gregory C.]

Hi Sudhir,

 

Looks like you made plastimatch crash.  That is not nice.

 

Are the data something you could share for testing?

 

Also, please let us know which plastimatch version.

 

Greg

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[Sudhir Pathak]

Hello Grey, 

Attached are three files: T1.nii (MPRAGE which I used to convert first into dicom format), thalamus_label49.nii (Masked ROI created from aseg.nii file, Label: 49). 

I am using 1.5.15 version:  

plastimatch convert --version 

Plastimatch version 1.5.15 (4523) 


Thanks a lot,

Sudhir

https://drive.google.com/file/d/0B_duz5DiNSCUeC1UYlRGYmplQ00/view?usp=sharing

https://drive.google.com/file/d/0B_duz5DiNSCUUnJGYmZvRGtDdWc/view?usp=sharing

[Sudhir Pathak]

Hello Greg, 

Attached are three files: T1.nii (MPRAGE which I used to convert first into dicom format), thalamus_label49.nii (Masked ROI created from aseg.nii file, Label: 49). 

I am using 1.5.15 version:  

plastimatch convert --version 

Plastimatch version 1.5.15 (4523) 


Thanks a lot,

Sudhir

https://drive.google.com/file/d/0B_duz5DiNSCUeC1UYlRGYmplQ00/view?usp=sharing

https://drive.google.com/file/d/0B_duz5DiNSCUUnJGYmZvRGtDdWc/view?usp=sharing

On Tuesday, November 17, 2015 at 7:55:27 PM UTC-5, Sharp, Gregory C. wrote:

[Sharp, Gregory C.]

Hi Sudhir,

Looks like the input-prefix option does not handle nifti.
I will investigate if this can be fixed.

Meanwhile, if you only have this one structure, you can do this:

plastimatch convert --referenced-ct T1_dicom --input-ss-img thalamus_label49.nii --output-dicom T1_dicom

Or, if you have multiple structures, convert them all to nrrd (or mha), like this:

plastimatch convert --input A.nii --output-img ROIs/A.nrrd
plastimatch convert --input B.nii --output-img ROIs/B.nrrd

and then proceed to use input-prefix.

Note also that your plastimatch version is pretty old.
I only tested on the current version (svn head).

Greg