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#1415 Fix PeRev directions#1416

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jan-petr merged 5 commits intodevelopfrom
bug-#1415_FixPErevDirections
May 17, 2023
Merged

#1415 Fix PeRev directions#1416
jan-petr merged 5 commits intodevelopfrom
bug-#1415_FixPErevDirections

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@jan-petr jan-petr commented May 16, 2023

Linked issue

Close #1415

@jan-petr jan-petr requested a review from HenkMutsaerts May 16, 2023 20:29
@jan-petr jan-petr self-assigned this May 16, 2023
@jan-petr jan-petr linked an issue May 16, 2023 that may be closed by this pull request
Identify PERev directions correctly #1415
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jan-petr commented May 16, 2023 •
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Issues with some Flavors...
COMPARISON TABLE:
flavor dataset name message
_____________________________________________ ____________________ __________________________ ______________________________________________________________________________

{'Philips_PCASL_2DEPI_3.2.1.1_dummyQUASAR_1'}    {'rawdata'         }    {'Missing file'          }    {'/sub-Sub1/perf/sub-Sub1_asl.json'                                          }
{'Philips_PCASL_2DEPI_3.2.1.1_dummyQUASAR_1'}    {'rawdata'         }    {'Missing file'          }    {'/sub-Sub1/perf/sub-Sub1_asl.nii.gz'                                        }
{'Philips_PCASL_2DEPI_3.2.1.1_dummyQUASAR_1'}    {'rawdata'         }    {'Missing file'          }    {'/sub-Sub1/perf/sub-Sub1_aslcontext.tsv'                                    }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'rawdataReference'}    {'Missing file'          }    {'/sub-SUB002/fmap/sub-SUB002_dir-lr_m0scan.json'                            }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'rawdataReference'}    {'Missing file'          }    {'/sub-SUB002/fmap/sub-SUB002_dir-lr_m0scan.nii.gz'                          }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'rawdataReference'}    {'Missing file'          }    {'/sub-SUB002/perf/sub-SUB002_dir-rl_m0scan.json'                            }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'rawdataReference'}    {'Missing file'          }    {'/sub-SUB002/perf/sub-SUB002_dir-rl_m0scan.nii.gz'                          }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'rawdata'         }    {'Missing file'          }    {'/sub-SUB002/fmap/sub-SUB002_dir-pa_m0scan.json'                            }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'rawdata'         }    {'Missing file'          }    {'/sub-SUB002/fmap/sub-SUB002_dir-pa_m0scan.nii.gz'                          }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'rawdata'         }    {'Missing file'          }    {'/sub-SUB002/perf/sub-SUB002_dir-ap_m0scan.json'                            }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'rawdata'         }    {'Missing file'          }    {'/sub-SUB002/perf/sub-SUB002_dir-ap_m0scan.nii.gz'                          }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'Both'            }    {'Different file content'}    {'Different file content: /sub-SUB002/perf/sub-SUB002_asl.json'              }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'rawdataReference'}    {'Missing file'          }    {'/sub-sub1100189/fmap/sub-sub1100189_dir-lr_run-1_m0scan.json'              }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'rawdataReference'}    {'Missing file'          }    {'/sub-sub1100189/fmap/sub-sub1100189_dir-lr_run-1_m0scan.nii.gz'            }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'rawdataReference'}    {'Missing file'          }    {'/sub-sub1100189/perf/sub-sub1100189_dir-rl_run-1_m0scan.json'              }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'rawdataReference'}    {'Missing file'          }    {'/sub-sub1100189/perf/sub-sub1100189_dir-rl_run-1_m0scan.nii.gz'            }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'rawdata'         }    {'Missing file'          }    {'/sub-sub1100189/fmap/sub-sub1100189_dir-pa_run-1_m0scan.json'              }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'rawdata'         }    {'Missing file'          }    {'/sub-sub1100189/fmap/sub-sub1100189_dir-pa_run-1_m0scan.nii.gz'            }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'rawdata'         }    {'Missing file'          }    {'/sub-sub1100189/perf/sub-sub1100189_dir-ap_run-1_m0scan.json'              }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'rawdata'         }    {'Missing file'          }    {'/sub-sub1100189/perf/sub-sub1100189_dir-ap_run-1_m0scan.nii.gz'            }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'Both'            }    {'Different file content'}    {'Different file content: /sub-sub1100189/perf/sub-sub1100189_run-1_asl.json'}
{'Siemens_PCASL_3DGRASE_XA31_multiPLD_2'    }    {'rawdataReference'}    {'Missing file'          }    {'/sub-1002/ses-1/fmap/sub-1002_ses-1_dir-ap_m0scan.json'                    }
{'Siemens_PCASL_3DGRASE_XA31_multiPLD_2'    }    {'rawdataReference'}    {'Missing file'          }    {'/sub-1002/ses-1/fmap/sub-1002_ses-1_dir-ap_m0scan.nii.gz'                  }
{'Siemens_PCASL_3DGRASE_XA31_multiPLD_2'    }    {'rawdata'         }    {'Missing file'          }    {'/sub-1002/ses-1/fmap/sub-1002_ses-1_dir-pa_m0scan.json'                    }
{'Siemens_PCASL_3DGRASE_XA31_multiPLD_2'    }    {'rawdata'         }    {'Missing file'          }    {'/sub-1002/ses-1/fmap/sub-1002_ses-1_dir-pa_m0scan.nii.gz'                  }
{'Siemens_PCASL_3DGRASE_XA31_multiPLD_2'    }    {'Both'            }    {'Different file content'}    {'Different file content: /sub-1002/ses-1/perf/sub-1002_ses-1_asl.json'      }
{'Philips_PCASL_2DEPI_3.2.1.1_dummyQUASAR_1'}    {'derivatives'     }    {'Missing file'          }    {'/ExploreASL/sub-Sub1_1/ASL_1/ASL4D.json'                                   }
{'Philips_PCASL_2DEPI_3.2.1.1_dummyQUASAR_1'}    {'derivatives'     }    {'Missing file'          }    {'/ExploreASL/sub-Sub1_1/ASL_1/ASL4D.nii.gz'                                 }
{'Philips_PCASL_2DEPI_3.2.1.1_dummyQUASAR_1'}    {'derivatives'     }    {'Missing file'          }    {'/ExploreASL/sub-Sub1_1/ASL_1/ASL4Dcontext.tsv'                             }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-SUB002_1/ASL_1/ASL4D.json'         }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-SUB002_1/ASL_1/M0.json'            }
{'Siemens_PCASL_3DGRASE_VB17A_TopUp_2'      }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-SUB002_1/ASL_1/M0_RevPE.json'      }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-sub1100189_1/ASL_1/ASL4D.json'     }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-sub1100189_1/ASL_1/M0.json'        }
{'Siemens_PCASL_3DGRASE_VE11C_DEBBIE_1'     }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-sub1100189_1/ASL_1/M0_RevPE.json'  }
{'Siemens_PCASL_3DGRASE_XA31_multiPLD_2'    }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-1002/ASL_1/ASL4D.json'             }
{'Siemens_PCASL_3DGRASE_XA31_multiPLD_2'    }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-1002/ASL_1/ASL4D_Source.json'      }
{'Siemens_PCASL_3DGRASE_XA31_multiPLD_2'    }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-1002/ASL_1/M0.json'                }
{'Siemens_PCASL_3DGRASE_XA31_multiPLD_2'    }    {'Both'            }    {'Different file content'}    {'Different file content: /ExploreASL/sub-1002/ASL_1/M0_RevPE.json'          }

LOGGING TABLE:

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jan-petr commented May 16, 2023

This was mostly fixing the LR vs AP order in flavors to update to the correct version.

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jan-petr commented May 16, 2023

All solved, but Philips_PCASL_2DEPI_3.2.1.1_dummyQUASAR_1 needs to be imported correctly

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jan-petr commented May 17, 2023

All fixed and the entire flavors work now.

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HenkMutsaerts approved these changes May 17, 2023
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Looks good. I don't know if it should be dir-si and dir-is, that was an educated guess :) But that seems fine according to BIDS.

We need to change the order for M0 so that it is i j k there as well (for readability).
We could also put this code in a subfunction.

Should we throw a warning if the phase encoding direction is not specified?

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jan-petr commented May 17, 2023

SI-IS was a good guess.

IJK order - will do. But not a sub, because for PERev - we need both normal and inverted to put as a reference field to JSON. So easier without a subfunction.

Yes - warning for missing direction!

@jan-petr jan-petr merged commit 82d94b2 into develop May 17, 2023
@jan-petr jan-petr deleted the bug-#1415_FixPErevDirections branch May 17, 2023 20:17
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Identify PERev directions correctly

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