Re: [Plastimatch] plastimatch convert rtss : error with --dicom-dir option
Paolo Zaffino
I usually use:
plastimatch convert --input=rtss.dcm --interpolation=nn --output-type=uchar --referenced-ct=ct_dicom_folder --output-prefix=folder_where_put_the_mha_files
HTH.
Best.
Paolo
On 10/05/2017 01:30 PM, Pierre Decazes wrote:
Hello,--
Hi would like to use this function to convert a RTSS to an nrrd or a mha:
plastimatch convert \ --input structures.dcm \ --output-ss-img outfile.nrrd \ --output-ss-list outfile.txt \ --dicom-dir ../ct-directory Described here : http://plastimatch.org/plastimatch.html However, the argument "--dicom-dir" is unknown ("Command line error: 'dicom-dir' is not a valid option"). I can run a simplified version without this optionbut the ROI obtained isn't in the same space than the original CT. When I run a simplified version with the CT in the same directory of the RTSS extracted, the same image is obtained. The two logs :piedec@piedec-Ubuntu:~$ plastimatch convert --input /media/piedec/2TO/RTSS/A1.rou.[...]478.1_00000.DCM --output-ss-img /media/piedec/2TO/RTSS/test.mha --output-ss-list /media/piedec/2TO/RTSS/test.txt
ITK exception.
itk::ImageFileReaderException (0x56332c182960)
Location: "unknown"
File: /usr/include/ITK-4.9/itkImageFileReader.hxx
Line: 143
Description: Could not create IO object for reading file /media/piedec/2TO/RTSS/A1[...].3189478.1_00000.DCM
Tried to create one of the following:
NiftiImageIO
NrrdImageIO
GiplImageIO
HDF5ImageIO
JPEGImageIO
GDCMImageIO
BMPImageIO
LSMImageIO
PNGImageIO
TIFFImageIO
VTKImageIO
StimulateImageIO
BioRadImageIO
MetaImageIO
MRCImageIO
GE4ImageIO
GE5ImageIO
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
Found RTSTUCT, UID=1.2.840[...].1505894494.2
Found DCM_ReferencedFrameOfReferenceSequence!
Found DCM_RTReferencedStudySequence!
Trying to load rt structure set.
Adding structure (1), 1
Adding structure (2), 2
Structure 1 has color 255\0\0
Structure 2 has color 255\0\0
Warning, slice spacing of RTSS may be unequal
-398.66 - -408.47 = 9.80994 vs. 3.26996
PIH is:
Origin = -127.564 -45.5323 -418.28
Size = 512 512 37
Spacing = 0.250339 0.250339 3.26996
Direction = 1 0 0 0 1 0 0 0 1
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.
Warning, slice spacing of RTSS may be unequal
-398.66 - -408.47 = 9.80994 vs. 3.26996
rast_dim = 512 512 37
rast_offset = -127.564 -45.5323 -418.28
rast_spacing = 0.250339 0.250339 3.26996
Rt_study_warp: warp and save ss.
Warp_and_save_ss: seg->rasterize
Setting use_ss_img_vec to true!
Rasterizing...
Converting...
Finished rasterization.
Warp_and_save_ss: save_ss_img
save_ss_img: save_ss_image
Trying to write image to /media/piedec/2TO/RTSS/test.mha
save_ss_img: save_ss_list
Done.
Finished!
piedec@piedec-Ubuntu:~$ plastimatch convert --input /media/piedec/2TO/RTSS/A1.[...]_00000.DCM --output-ss-img /media/piedec/2TO/RTSS/test2.mha --output-ss-list /media/piedec/2TO/RTSS/test.txt
ITK exception.
itk::ImageFileReaderException (0x5628ae2d7960)
Location: "unknown"
File: /usr/include/ITK-4.9/itkImageFileReader.hxx
Line: 143
Description: Could not create IO object for reading file /media/piedec/2TO/RTSS/A1.[...]_00000.DCM
Tried to create one of the following:
NiftiImageIO
NrrdImageIO
GiplImageIO
HDF5ImageIO
JPEGImageIO
GDCMImageIO
BMPImageIO
LSMImageIO
PNGImageIO
TIFFImageIO
VTKImageIO
StimulateImageIO
BioRadImageIO
MetaImageIO
MRCImageIO
GE4ImageIO
GE5ImageIO
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
Found RTSTUCT, UID=1.2.840.[..].1505894494.2
Found DCM_ReferencedFrameOfReferenceSequence!
Found DCM_RTReferencedStudySequence!
Trying to load rt structure set.
Adding structure (1), 1
Adding structure (2), 2
Structure 1 has color 255\0\0
Structure 2 has color 255\0\0
Warning, slice spacing of RTSS may be unequal
-398.66 - -408.47 = 9.80994 vs. 3.26996
PIH is:
Origin = -127.564 -45.5323 -418.28
Size = 512 512 37
Spacing = 0.250339 0.250339 3.26996
Direction = 1 0 0 0 1 0 0 0 1
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.
Warning, slice spacing of RTSS may be unequal
-398.66 - -408.47 = 9.80994 vs. 3.26996
rast_dim = 512 512 37
rast_offset = -127.564 -45.5323 -418.28
rast_spacing = 0.250339 0.250339 3.26996
Rt_study_warp: warp and save ss.
Warp_and_save_ss: seg->rasterize
Setting use_ss_img_vec to true!
Rasterizing...
Converting...
Finished rasterization.
Warp_and_save_ss: save_ss_img
save_ss_img: save_ss_image
Trying to write image to /media/piedec/2TO/RTSS/test2.mha
save_ss_img: save_ss_list
Done.
Finished!I would like to have the ROI in the same space than the referenced CT. Do you have a solution for this problem, please ? Thanks
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Sharp, Gregory C.
It seems the documentation is in error. As Paolo pointed out the correct usage is “referenced-ct” instead of “dicom-dir”. I have updated the document.
By the way the --interpolation=nn is not needed. It is the default.
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Sharp, Gregory C.
Sorry to respond to myself. If your structure set and CT image are in the same directory, it is simpler. No need for referenced-ct option. Just specify the input directory like this:
plastimatch convert --input dicom/ --output-ss-image output.nrrd ## or use --output-prefix