Add a XA60 file, a test and documentation for PatientAgeDerived

Author: marcelzwiers

docs/_static/dictionary-custom.txt

@@ -75,18 +75,19 @@ Nibabel2bids
 Oostenveld
 OpenMR
 P7
-Pt018
-Pt019
-PET2BIDS
+PatientAge
+PatientComments
 PatientName
 PatientSex
 Pawlik
-PatientComments
+PET2BIDS
 PerformedProcedureStepDescription
 Pet2bids
 Prepend
 ProtocolName
 PsychoPy
+Pt018
+Pt019
 PULS
 PyQt5
 Pydeface

docs/plugins.rst

@@ -12,7 +12,7 @@ You can use the ``bidscoin`` utility to list, install or uninstall BIDScoin plug
 Dcm2niix2bids: a plugin for DICOM and PAR/REC data
 --------------------------------------------------
 
-The 'dcm2niix2bids' plugin is a wrapper around the well-known pydicom, nibabel and (in particular) `dcm2niix <https://github.com/rordenlab/dcm2niix>`__ tools to interact with and convert DICOM and Philips SPAR/REC source data. Pydicom is used to read DICOM attributes, nibabel is used to read PAR attribute values and dcm2niix is used to convert the DICOM and PAR/REC source data to NIfTI and create BIDS sidecar files. Personal data from the source header (e.g. Age, Sex) is added to the BIDS participants.tsv file. Please cite: `DOI: 10.1016/j.jneumeth.2016.03.001 <https://doi.org/10.1016/j.jneumeth.2016.03.001>`__
+The 'dcm2niix2bids' plugin is a wrapper around the well-known pydicom, nibabel and (in particular) `dcm2niix <https://github.com/rordenlab/dcm2niix>`__ tools to interact with and convert DICOM and Philips SPAR/REC source data. Pydicom is used to read DICOM attributes, nibabel is used to read PAR attribute values and dcm2niix is used to convert the DICOM and PAR/REC source data to NIfTI and create BIDS sidecar files. Personal data from the source header (e.g. Age, Sex) is added to the BIDS participants.tsv file. The plugin supports a custom tag ``PatientAgeDerived``, which computes age with high precision by taking the difference between ``AcquisitionDate`` and ``BirthDate``. Please cite: `DOI: 10.1016/j.jneumeth.2016.03.001 <https://doi.org/10.1016/j.jneumeth.2016.03.001>`__
 
 Spec2nii2bids: a plugin for MR spectroscopy data
 ------------------------------------------------

docs/troubleshooting.rst

@@ -109,8 +109,8 @@ The bidscoiner says that the IntendedFor search gave no results
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Even if you have specified the IntendedFor value in the bidseditor, you still get `"Empty 'IntendedFor' field map value in {..}: the search for {..} gave no results"`. This may be because you hardcoded the IntendedFor value instead of providing a search pattern. Or it may be that you provided a correct search pattern but that for some subjects the target images were not acquired or could not be found (e.g. due to irregularities in the acquisition). Check out the BIDS output session(s) mentioned in the warning(s) and see if and how you should update your IntendedFor search pattern accordingly.
 
-The bidscoiner says that I need to check my scan.tsv files
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+The bidscoiner says that I need to check my scans.tsv files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 This may occur when you use a dynamic run-index (e.g. ``<<>>`` or ``<<1>>``) and the folder names of your DICOM Series do not start with the DICOM SeriesNumber (this is default on Siemens). The solution would be to rename your Series folder to alphabetical order (in many cases this can be done with ``disomsort``), or to use another dynamic value, e.g. ``<<SeriesNumber>>`` (the latter will yield properly ordered run-indices, albeit with a variable step, e.g. yielding ``run-2`` + ``run-5`` instead of ``run-1`` + ``run-2``
 
 I use dynamic run-indices and now have 'orphan' run-indices in my BIDS directory
@@ -126,6 +126,10 @@ You can simply use the ``bidseditor`` to make changes to your bidsmap, delete al
    $ bidsmapper bidsfolder bidsfolder_new -p nibabel2bids -t bidsmap_bids2bids
    $ bidscoiner bidsfolder bidsfolder_new
 
+I have set ``anon: n``, but I still get rounded "PatientAge" numbers
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+In DICOM, ``PatientAge`` can be stored in `days, weeks, months or years <https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html>`__. So probably your ``PatientAge`` data was stored in years. To get a decimal age data, you can use the custom ``PatientAgeDerived`` tag from the `dcm2niix2bids plugin <./plugins.html#dcm2niix2bids>`__.
+
 Irregular data acquisition
 --------------------------
 

tests/test_bids.py

@@ -18,6 +18,11 @@ def dcm_file():
     return Path(get_testdata_file('MR_small.dcm'))
 
 
+@pytest.fixture(scope='module')
+def dcm_xa60_file(test_data):
+    return Path(test_data/'XA60'/'00001_1.3.12.2.1107.5.2.43.66068.30000024121907551118800028571.IMA')
+
+
 @pytest.fixture(scope='module')
 def dicomdir():
     return Path(get_testdata_file('DICOMDIR'))
@@ -57,6 +62,11 @@ def test_attributes(self, datasource, extdatasource):
         assert datasource.attribute(r'PatientName:.*\^(.*?)1') == 'MR'         # PatientName = 'CompressedSamples^MR1'
         assert extdatasource.attribute('PatientName') == 'ExtendedAttributesTest'
 
+    def test_age_derived(self, dcm_xa60_file):
+        datasource = DataSource(dcm_xa60_file, {'dcm2niix2bids': Plugin({})}, 'DICOM')
+        assert datasource.attribute('PatientAge') == '036Y'
+        assert datasource.attribute('PatientAgeDerived') == '36.36139630390144'
+
     @pytest.mark.parametrize('subid',  ['sub-001', 'pat^visit'])
     @pytest.mark.parametrize('sesid',  ['ses-01',  'visit^01', ''])
     @pytest.mark.parametrize('subprefix', ['sub-', 'pat^', '*'])