Converting XML/REC files

[po09i]

Hello!

I have seen in the BIDScoin article and in your documentation that conversion from XML/REC is supported. I have been trying to convert XML/REC files from Philips into NIfTIs. I tried using PAR/REC files and I was able to get it working, but using the XML header file, rather than the PAR header file will not work. Here is my error message:

$ bidsmapper ./bids/sourcedata ./bids

INFO | 
INFO | -------------- START BIDSmapper ------------
INFO | >>> bidsmapper sourcefolder=./bids/sourcedata bidsfolder=./bids bidsmap=bidsmap.yaml template=/opt/homebrew/lib/python3.11/site-packages/bidscoin/heuristics/bidsmap_dccn.yaml plugins=[] subprefix=None sesprefix=None store=False force=False
INFO | Reading: ./bids/code/bidscoin/bidsmap.yaml
INFO | Checking the bidsmap run-items:
INFO | Could not validate every run-item in the bidsmap
INFO | Reading: /opt/homebrew/lib/python3.11/site-packages/bidscoin/heuristics/bidsmap_dccn.yaml
INFO | Checking the bidsmap run-items:
INFO | Could not validate every run-item in the bidsmap
INFO | Mapping: ./bids/sourcedata/sub-test1 (subject 1/1)                                                                  
VERBOSE | Ignoring hidden file: ./bids/sourcedata/sub-test1/.DS_Store                                                      
VERBOSE | Executing plugin: dcm2niix2bids.py -> ./bids/sourcedata/sub-test1                                                
VERBOSE | Ignoring hidden file: ./bids/sourcedata/sub-test1/.DS_Store                                                      
VERBOSE | Importing plugin: '/opt/homebrew/lib/python3.11/site-packages/bidscoin/plugins/dcm2niix2bids.py'                                                                                                  
VERBOSE | Ignoring hidden file: ./bids/sourcedata/sub-test1/.DS_Store                                                      
VERBOSE | Importing plugin: '/opt/homebrew/lib/python3.11/site-packages/bidscoin/plugins/dcm2niix2bids.py'                                                                                                  
  0%|                                                                                                                                                                            | 0/1 [00:00<?, ?subject/s]/opt/homebrew/lib/python3.11/site-packages/nibabel/parrec.py:517: UserWarning: PAR/REC version 'None' is currently not supported -- making an attempt to read nevertheless. Please email the NiBabel mailing list, if you are interested in adding support for this version. 
  warnings.warn(
WARNING | Could not parse series_type from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                       
None
WARNING | Could not parse exam_name from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                         
None
WARNING | Could not parse protocol_name from /./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                     
None
WARNING | Could not parse tech from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                              
None
WARNING | Could not parse diffusion from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                         
None
WARNING | Could not parse fov from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                               
None
WARNING | Could not parse scan_resolution from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                   
None
WARNING | Could not parse scan_mode from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                         
None
WARNING | Could not parse max_slices from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                        
None
WARNING | Could not parse flow_compensation from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                 
None
WARNING | Could not parse max_echoes from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                        
None
WARNING | Could not parse repetition_time from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                   
None
WARNING | Could not parse prep_direction from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                    
None
WARNING | Could not parse MRAcquisitionType from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                 
None
WARNING | Could not parse ProtocolName from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                      
None
INFO | Discovered 'extra_data' PAR sample: ./bids/sourcedata/sub-test1/DBIEX_1_1.xml                                       
INFO | Opening the bidseditor                                                                                                                                                                               
WARNING | Could not parse filepath from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
INFO | -------------- FINISHED! -------------------
INFO | 
INFO | The following BIDScoin errors and warnings were reported:

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
2023-09-04 15:39:17 - WARNING | Could not parse series_type from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse exam_name from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse protocol_name from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse tech from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse diffusion from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse fov from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse scan_resolution from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse scan_mode from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse max_slices from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse flow_compensation from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse max_echoes from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse repetition_time from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse prep_direction from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse MRAcquisitionType from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:17 - WARNING | Could not parse ProtocolName from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
2023-09-04 15:39:18 - WARNING | Could not parse filepath from ./bids/sourcedata/sub-test1/DBIEX_1_1.xml
None
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

INFO | For the complete log see: ./bids/code/bidscoin/bidsmapper.log
NB: That folder may contain privacy sensitive information, e.g. pathnames in logfiles and provenance data samples

Note: I edited the paths to make them relative to the bids folder rather than displaying the full path.

Perhaps you have an XML/REC dataset along with instructions to get the conversion working that I could follow to help me understand what I am doing wrong? Thanks! :)

[marcelzwiers]

Hello Alex, thanks for your report. I work with Siemens DICOM data and don't have XML/REC data to test my code, hence your problems. I suspect I can use nibabel to solve it, will look into it...

[marcelzwiers]

I had a look and I was already using nibabel to read the PAR/XML header, assuming nibabel was supporting XML. It turns out that is an open issue/PR:
nipy/nibabel#681
nipy/nibabel#683

BIDScoin does support XML/REC for spectroscopy btw (SPAR)

[marcelzwiers]

I see there is another hurdle, namely dcm2niix doesn't like XML/REC:

About

dcm2niix attempts to convert Philips PAR/REC format images to NIfTI. While this format remains popular with users, it is slowly being superseded by Philips enhanced DICOM format, an XML/REC format as well as the direct NIfTI export. Note that dcm2niix does not support the XML/REC format.

[marcelzwiers]

I will update the docs to state that only SPAR-XML is supported

[po09i]

Thanks for the quick feedback!