Closes #923 Subject ID format by MichaelStritt · Pull Request #944 · ExploreASL/ExploreASL

MichaelStritt · 2021-11-25T08:37:28Z

Linked issue

Check out #923

How to test

Run the flavors import.

MichaelStritt · 2021-11-26T09:37:25Z

@jan-petr: Please have a look at d4e689b. It is supposed to help with modularity & getting the subject id to the bids format. DCM2NII depends on the sourceStructure.json, but NII2BIDS, Deface and BIDS2Legacy have to be independent. This should work with this commit. In addition, the subject IDs are made BIDS compliant within DCM2NII now. This is done using an "export id" for the directory name. Think the code is quite clean and helps with comments from here and is somewhat related to this.

MichaelStritt · 2021-11-26T09:54:57Z

@jan-petr: This is kind of related to #945, so it would be nice to merge this (maybe today?), so that I can get some work done for #945. I'm testing right now if #923 doesn't break other flavors.

jan-petr

Minor reporting comment.

Modules/SubModule_Import/xASL_imp_DCM2NII_Subject.m

MichaelStritt · 2021-11-26T11:25:53Z

@jan-petr: Okay, so if we ignore the PAR REC datasets and the Hadamards as well, then there's only a few left.

COMPARISON TABLE:
                        flavor                                dataset                      name                                            message                              
    _______________________________________________    ______________________    ________________________    ___________________________________________________________________

    'Philips_PCASL_2DEPI_3.2.2.1_2'                    'Both'                    'Different file content'    'Different file content: dataset_description.json'                 
    'Philips_PCASL_2DEPI_PARREC_1'                     'rawdata'                 'Missing folder'            '\sub-Sub01\ses-1\anat'                                            
    'Philips_PCASL_2DEPI_PARREC_1'                     'rawdata'                 'Missing file'              '\sub-Sub01\ses-1\anat\sub-Sub01_ses-1_T1w.json'                   
    'Philips_PCASL_2DEPI_PARREC_1'                     'rawdata'                 'Missing file'              '\sub-Sub01\ses-1\anat\sub-Sub01_ses-1_T1w.nii.gz'                 
    'Philips_PCASL_2DEPI_PARREC_1'                     'rawdata'                 'Missing file'              '\sub-Sub01\ses-1\perf\sub-Sub01_ses-1_asl.json'                   
    'Philips_PCASL_2DEPI_PARREC_1'                     'rawdata'                 'Missing file'              '\sub-Sub01\ses-1\perf\sub-Sub01_ses-1_asl.nii.gz'                 
    'Philips_PCASL_2DEPI_PARREC_1'                     'rawdata'                 'Missing file'              '\sub-Sub01\ses-1\perf\sub-Sub01_ses-1_aslcontext.tsv'             
    'Philips_PCASL_2DEPI_PARREC_2'                     'rawdata'                 'Missing file'              '\sub-Sub01\perf\sub-Sub01_asl.json'                               
    'Philips_PCASL_2DEPI_PARREC_2'                     'rawdata'                 'Missing file'              '\sub-Sub01\perf\sub-Sub01_asl.nii.gz'                             
    'Philips_PCASL_2DEPI_PARREC_2'                     'rawdata'                 'Missing file'              '\sub-Sub01\perf\sub-Sub01_aslcontext.tsv'                         
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_asl.json'                                 
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_asl.nii.gz'                               
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_aslcontext.tsv'                           
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_m0scan.json'                              
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_m0scan.nii.gz'                            
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_asl.json'                                 
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_asl.nii.gz'                               
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_aslcontext.tsv'                           
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_m0scan.json'                              
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'rawdata'                 'Missing file'              '\sub-Sub1\perf\sub-Sub1_m0scan.nii.gz'                            
    'GE_PCASL_3Dspiral_24.0LX_WIP_1'                   'derivativesReference'    'Missing folder'            '\ExploreASL\temp'                                                 
    'GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1'      'derivativesReference'    'Missing file'              '\ExploreASL\sub-001\ASL_1\ASL4D.nii.gz'                           
    'GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1'      'derivativesReference'    'Missing file'              '\ExploreASL\sub-001\ASL_1\ASL4D_aslcontext.tsv'                   
    'GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-001\ASL_1\ASL4D.nii'                              
    'GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-001\ASL_1\ASL4D_Source.json'                      
    'GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-001\ASL_1\ASL4D_Source.nii'                       
    'GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-001\ASL_1\ASL4D_Source_aslcontext.tsv'            
    'GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-001\ASL_1\M0.json'                                
    'GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-001\ASL_1\M0.nii'                                 
    'GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1'      'Both'                    'Different file content'    'Different file content: \ExploreASL\sub-001\ASL_1\ASL4D.json'     
    'Philips_PASL_2DEPI_5.4.1.0_ADNI3_006_S_6681_1'    'Both'                    'Different file content'    'Different file content: \ExploreASL\sub-001\ASL_1\ASL4D.json'     
    'Philips_PCASL_2DEPI_3.2.2.1_2'                    'derivativesReference'    'Missing folder'            '\ExploreASL\temp'                                                 
    'Philips_PCASL_2DEPI_3.2.2.1_2'                    'Both'                    'Different file content'    'Different file content: \ExploreASL\dataset_description.json'     
    'Philips_PCASL_2DEPI_3.2.2.1_2'                    'Both'                    'Different file content'    'Different file content: \ExploreASL\sub-EMI301_1\ASL_1\ASL4D.json'
    'Philips_PCASL_2DEPI_3.2.2.1_2'                    'Both'                    'Different file content'    'Different file content: \ExploreASL\sub-EMI301_1\ASL_1\M0.json'   
    'Philips_PCASL_2DEPI_3.2.2.1_2'                    'Both'                    'Different file content'    'Different file content: \ExploreASL\sub-EMI301_1\FLAIR.json'      
    'Philips_PCASL_2DEPI_3.2.2.1_2'                    'Both'                    'Different file content'    'Different file content: \ExploreASL\sub-EMI301_1\T1.json'         
    'Philips_PCASL_2DEPI_5.1.9.1_GMB_1'                'derivativesReference'    'Missing folder'            '\ExploreASL\temp'                                                 
    'Philips_PCASL_2DEPI_PARREC_1'                     'derivativesReference'    'Missing folder'            '\ExploreASL\temp'                                                 
    'Philips_PCASL_2DEPI_PARREC_1'                     'derivatives'             'Missing folder'            '\ExploreASL\sub-Sub01\ASL_1'                                      
    'Philips_PCASL_2DEPI_PARREC_1'                     'derivativesReference'    'Missing file'              '\ExploreASL\temp\dcm2niiCatchedErrors.json'                       
    'Philips_PCASL_2DEPI_PARREC_1'                     'derivativesReference'    'Missing file'              '\ExploreASL\temp\dcm2niiCatchedErrors.mat'                        
    'Philips_PCASL_2DEPI_PARREC_1'                     'derivatives'             'Missing file'              '\ExploreASL\sub-Sub01\ASL_1\ASL4D.json'                           
    'Philips_PCASL_2DEPI_PARREC_1'                     'derivatives'             'Missing file'              '\ExploreASL\sub-Sub01\ASL_1\ASL4D.nii.gz'                         
    'Philips_PCASL_2DEPI_PARREC_1'                     'derivatives'             'Missing file'              '\ExploreASL\sub-Sub01\ASL_1\ASL4D_aslcontext.tsv'                 
    'Philips_PCASL_2DEPI_PARREC_1'                     'derivatives'             'Missing file'              '\ExploreASL\sub-Sub01\T1.json'                                    
    'Philips_PCASL_2DEPI_PARREC_1'                     'derivatives'             'Missing file'              '\ExploreASL\sub-Sub01\T1.nii.gz'                                  
    'Philips_PCASL_2DEPI_PARREC_2'                     'derivativesReference'    'Missing folder'            '\ExploreASL\temp'                                                 
    'Philips_PCASL_2DEPI_PARREC_2'                     'derivatives'             'Missing folder'            '\ExploreASL\sub-Sub01_1\ASL_1'                                    
    'Philips_PCASL_2DEPI_PARREC_2'                     'derivativesReference'    'Missing file'              '\ExploreASL\temp\dcm2niiCatchedErrors.json'                       
    'Philips_PCASL_2DEPI_PARREC_2'                     'derivativesReference'    'Missing file'              '\ExploreASL\temp\dcm2niiCatchedErrors.mat'                        
    'Philips_PCASL_2DEPI_PARREC_2'                     'derivatives'             'Missing file'              '\ExploreASL\sub-Sub01_1\ASL_1\ASL4D.json'                         
    'Philips_PCASL_2DEPI_PARREC_2'                     'derivatives'             'Missing file'              '\ExploreASL\sub-Sub01_1\ASL_1\ASL4D.nii.gz'                       
    'Philips_PCASL_2DEPI_PARREC_2'                     'derivatives'             'Missing file'              '\ExploreASL\sub-Sub01_1\ASL_1\ASL4D_aslcontext.tsv'               
    'Philips_PCASL_3DGRASE_5.4.0.2_1'                  'derivativesReference'    'Missing folder'            '\ExploreASL\temp'                                                 
    'Siemens_PASL_2DEPI_VB15A_ADNI2_941_S_4764_1'      'Both'                    'Different file content'    'Different file content: \ExploreASL\dataPar.json'                 
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'derivativesReference'    'Missing folder'            '\ExploreASL\temp'                                                 
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'derivatives'             'Missing folder'            '\ExploreASL\sub-Sub1_1\ASL_1'                                     
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'derivativesReference'    'Missing file'              '\ExploreASL\temp\dcm2niiCatchedErrors.json'                       
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'derivativesReference'    'Missing file'              '\ExploreASL\temp\dcm2niiCatchedErrors.mat'                        
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\ASL4D.json'                          
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\ASL4D.nii.gz'                        
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\ASL4D_aslcontext.tsv'                
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\M0.json'                             
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard4-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\M0.nii.gz'                           
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'derivativesReference'    'Missing folder'            '\ExploreASL\temp'                                                 
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'derivatives'             'Missing folder'            '\ExploreASL\sub-Sub1_1\ASL_1'                                     
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'derivativesReference'    'Missing file'              '\ExploreASL\temp\dcm2niiCatchedErrors.json'                       
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'derivativesReference'    'Missing file'              '\ExploreASL\temp\dcm2niiCatchedErrors.mat'                        
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\ASL4D.json'                          
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\ASL4D.nii.gz'                        
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\ASL4D_aslcontext.tsv'                
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\M0.json'                             
    'Siemens_PCASL_3DGRASE_VD13A_Hadamard8-FME_1'      'derivatives'             'Missing file'              '\ExploreASL\sub-Sub1_1\ASL_1\M0.nii.gz'                           
    'Siemens_PCASL_3DGRASE_VE11C_1'                    'derivativesReference'    'Missing folder'            '\ExploreASL\temp'                                                 

LOGGING TABLE:

Siemens_PCASL_3DGRASE_VE11C_1: Seems like it just didn't fully delete temp. The directory is there but it is empty.
Philips_PCASL_3DGRASE_5.4.0.2_: Same here.
Philips_PCASL_2DEPI_5.1.9.1_GMB_1: Same here.
GE_PCASL_3Dspiral_24.0LX_WIP_1: Same here.
Philips_PCASL_2DEPI_3.2.2.1_2: Seems like here there's just the version information of ExploreASL in the JSONs and that one differs.
GE_PCASL_3Dspiral_25.0LX_ADNI3_027_S_5079_1: Weirdly the ASL4D source NIFTI isn't there and the M0 is missing too, did we change something there?

jan-petr

OK.

DCM2NII depends on sourceStructure.json, but NII2BIDS, Deface and BIDS2Legacy have to be independent. This should work with this commit. In addition, the subject IDs are made BIDS compliant within DCM2NII now.

MichaelStritt requested a review from jan-petr November 25, 2021 08:37

MichaelStritt self-assigned this Nov 25, 2021

MichaelStritt linked an issue Nov 25, 2021 that may be closed by this pull request

BIDS2Legacy issue with certain subject names #923

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MichaelStritt added the import Related to data import module label Nov 25, 2021

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MichaelStritt changed the title ~~Closes #923 (Subject ID format)~~ Closes #923 Subject ID format Nov 26, 2021

jan-petr requested changes Nov 26, 2021

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Modules/SubModule_Import/xASL_imp_DCM2NII_Subject.m Outdated Show resolved Hide resolved

MichaelStritt requested a review from jan-petr November 26, 2021 10:12

jan-petr approved these changes Nov 26, 2021

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MichaelStritt added 3 commits November 26, 2021 12:31

#923 xASL_adm_CorrectName: fix formatting, add option

2cd35b7

#923 xASL_imp_...: modularity & bids format

8d8c3d3

DCM2NII depends on sourceStructure.json, but NII2BIDS, Deface and BIDS2Legacy have to be independent. This should work with this commit. In addition, the subject IDs are made BIDS compliant within DCM2NII now.

#923 xASL_imp_DCM2NII_Subject: improve feedback

1ae5b03

MichaelStritt force-pushed the bug-#923_SubjectMissingBIDS2Legacy branch from 2511317 to 1ae5b03 Compare November 26, 2021 11:32

MichaelStritt merged commit 1ae5b03 into develop Nov 26, 2021

MichaelStritt deleted the bug-#923_SubjectMissingBIDS2Legacy branch November 26, 2021 11:33

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Closes #923 Subject ID format#944

Closes #923 Subject ID format#944
MichaelStritt merged 3 commits intodevelopfrom
bug-#923_SubjectMissingBIDS2Legacy

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