UNFmontreal · arnaudbore · Jun 12, 2023 · Jun 8, 2023 · Jun 8, 2023 · Jun 8, 2023
diff --git a/dcm2bids/acquisition.py b/dcm2bids/acquisition.py
@@ -26,8 +26,8 @@ def __init__(
         participant,
         dataType,
         modalityLabel,
-        indexSidecar=None,
         customLabels="",
+        id=None,
         srcSidecar=None,
         sidecarChanges=None,
         intendedFor=None,
@@ -38,9 +38,9 @@ def __init__(
 
         self._modalityLabel = ""
         self._customLabels = ""
+        self._id = ""
         self._intendedFor = None
-        self._indexSidecar = None
-
+
         self.participant = participant
         self.dataType = dataType
         self.modalityLabel = modalityLabel
@@ -57,6 +57,11 @@ def __init__(
         else:
             self.intendedFor = intendedFor
 
+        if id is None:
+            self.id = None
+        else:
+            self.id = id
+
         self.dstFile = ''
 
     def __eq__(self, other):
@@ -79,6 +84,18 @@ def modalityLabel(self, modalityLabel):
         """ Prepend '_' if necessary"""
         self._modalityLabel = self.prepend(modalityLabel)
 
+    @property
+    def id(self):
+        """
+        Returns:
+            A string '_<id>'
+        """
+        return self._id
+
+    @id.setter
+    def id(self, value):
+        self._id = value
+
     @property
     def customLabels(self):
         """
@@ -191,23 +208,7 @@ def intendedFor(self, value):
         else:
             self._intendedFor = [value]
 
-    @property
-    def indexSidecar(self):
-        """
-        Returns:
-            A int '_<indexSidecar>'
-        """
-        return self._indexSidecar
-
-    @indexSidecar.setter
-    def indexSidecar(self, value):
-        """
-        Returns:
-            A int '_<indexSidecar>'
-        """
-        self._indexSidecar = value
-
-    def dstSidecarData(self, descriptions, intendedForList):
+    def dstSidecarData(self, intendedForList):
         """
         """
         data = self.srcSidecar.origData
@@ -218,7 +219,11 @@ def dstSidecarData(self, descriptions, intendedForList):
             intendedValue = []
 
             for index in self.intendedFor:
-                intendedValue = intendedValue + intendedForList[index]
+                if (isinstance(index, int)):
+                    logging.error('Dcm2bids (>=3.0.0) does not support indexing anymore for intendedFor field.\n'
+                                  f'Please check {DEFAULT.link_doc_intended_for}')
+                else:
+                    intendedValue = intendedValue + intendedForList[index]
 
             if len(intendedValue) == 1:
                 data["IntendedFor"] = intendedValue[0]

diff --git a/dcm2bids/dcm2bids_gen.py b/dcm2bids/dcm2bids_gen.py
@@ -4,7 +4,6 @@
 Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
 """
 
-import argparse
 import logging
 import os
 from pathlib import Path
@@ -133,10 +132,10 @@ def run(self):
 
         self.logger.info("moving acquisitions into BIDS folder")
 
-        intendedForList = [[] for i in range(len(parser.descriptions))]
+        intendedForList = {}
         for acq in parser.acquisitions:
             acq.setDstFile()
-            intendedForList = self.move(acq, intendedForList)
+            self.move(acq, intendedForList, dcm2niix.options)
 
         if self.bids_validate:
             try:
@@ -149,10 +148,9 @@ def run(self):
                                  "bids-validator may not been installed on your computer"
                                  f"Please check: https://github.com/bids-standard/bids-validator#quickstart")
 
-    def move(self, acquisition, intendedForList):
+    def move(self, acquisition, intendedForList, dcm2niix_options):
         """Move an acquisition to BIDS format"""
         for srcFile in glob(acquisition.srcRoot + ".*"):
-
             ext = Path(srcFile).suffixes
             ext = [curr_ext for curr_ext in ext if curr_ext in ['.nii', '.gz',
                                                                 '.json',
@@ -174,7 +172,7 @@ def move(self, acquisition, intendedForList):
                     continue
 
             # it's an anat nifti file and the user using a deface script
-            if (self.config.get("defaceTpl") and acquisition.dataType == "func" and ".nii" in ext):
+            if (self.config.get("defaceTpl") and acquisition.dataType == "anat" and ".nii" in ext):
                 try:
                     os.remove(dstFile)
                 except FileNotFoundError:
@@ -185,20 +183,27 @@ def move(self, acquisition, intendedForList):
                 cmd = [w.replace('dstFile', dstFile) for w in defaceTpl]
                 run_shell_command(cmd)
 
-                intendedForList[acquisition.indexSidecar].append(acquisition.dstIntendedFor + "".join(ext))
+                intendedForList[acquisition.id] = acquisition.dstIntendedFor + "".join(ext)
 
             elif ".json" in ext:
-                data = acquisition.dstSidecarData(self.config["descriptions"],
-                                                  intendedForList)
+                data = acquisition.dstSidecarData(intendedForList)
                 save_json(dstFile, data)
                 os.remove(srcFile)
 
             # just move
             else:
                 os.rename(srcFile, dstFile)
 
-            intendedFile = acquisition.dstIntendedFor + ".nii.gz"
-            if intendedFile not in intendedForList[acquisition.indexSidecar]:
-                intendedForList[acquisition.indexSidecar].append(intendedFile)
+            curr_img_ext = '.nii.gz'
+            if '-z n' in dcm2niix_options:
+                curr_img_ext = '.nii'
+
+            intendedFile = acquisition.dstIntendedFor + curr_img_ext
+            if acquisition.id:
+                if acquisition.id in intendedForList:
+                    if intendedFile not in intendedForList[acquisition.id]:
+                        intendedForList[acquisition.id] =  intendedForList[acquisition.id] + intendedFile
+                else:
+                    intendedForList[acquisition.id] = [intendedFile]
 
         return intendedForList
diff --git a/dcm2bids/sidecar.py b/dcm2bids/sidecar.py
@@ -226,7 +226,6 @@ def build_acquisitions(self, participant):
                 desc = valid_descriptions[0]
                 acq = Acquisition(participant,
                                   srcSidecar=sidecar, **desc)
-                acq.indexSidecar = self.descriptions.index(desc)
                 acq.setDstFile()
 
                 if acq.intendedFor != [None]:
@@ -245,7 +244,6 @@ def build_acquisitions(self, participant):
                 self.logger.warning("Several Pairing  <-  %s", sidecarName)
                 for desc in valid_descriptions:
                     acq = Acquisition(participant,
-                                      indexSidecar=self.descriptions.index(desc),
                                       **desc)
                     self.logger.warning("    ->  %s", acq.suffix)
 

diff --git a/dcm2bids/utils/utils.py b/dcm2bids/utils/utils.py
@@ -14,7 +14,8 @@ class DEFAULT(object):
     doc = "Documentation at https://unfmontreal.github.io/Dcm2Bids/"
 
     link_bids_validator = "https://github.com/bids-standard/bids-validator#quickstart"
-
+    link_doc_intended_for = "https://unfmontreal.github.io/Dcm2Bids/docs/tutorial/first-steps/#populating-the-config-file"
+
     # cli dcm2bids
     cliSession = ""
     cliOutputDir = os.getcwd()

diff --git a/docs/how-to/create-config-file.md b/docs/how-to/create-config-file.md
@@ -17,6 +17,7 @@
       }
     },
     {
+      "id": "task-rest",
       "dataType": "func",
       "modalityLabel": "bold",
       "customLabels": "task-rest",
@@ -28,12 +29,13 @@
     {
       "dataType": "fmap",
       "modalityLabel": "fmap",
-      "intendedFor": 1,
+      "intendedFor": "task_rest",
       "criteria": {
         "ProtocolName": "*field_mapping*"
       }
     },
     {
+      "id": "id_task_learning",
       "dataType": "func",
       "modalityLabel": "bold",
       "customLabels": "task-learning",
@@ -50,7 +52,7 @@
       "criteria": {
         "SeriesDescription": "fmap_task-learning"
       },
-      "IntendedFor": 2,
+      "IntendedFor": "id_task_learning",
       "sidecarChanges": {
         "TaskName": "learning"
       }
@@ -148,13 +150,11 @@ Optional field to change or add information in a sidecar.
 
 ## intendedFor
 
-Optional field to add an `IntendedFor` entry in the sidecar of a fieldmap. Just
-put the index or a list of indices of the description(s) that's intended for.
-
-Python index begins at `0` so in the example, **`1`** means it is intended for
-`task-rest_bold` and **`2`** is intended for `task-learning` which will be
-renamed to only `learning` because of the
-`"sidecarChanges": { "TaskName": "learning" }` field.
+Optional field to add an `IntendedFor` entry in the sidecar of a fieldmap. 
+You will need to set an id to the corresponding description and put the same id in the `IntendedFor` field.
+Fo example, **`task_rest`** means it is intended for `task-rest_bold` 
+and **`id_task_learning`** is intended for `task-learning` which will be
+renamed to only `learning` because of the `"sidecarChanges": { "TaskName": "learning" }` field.
 
 ## Multiple config files
 

diff --git a/docs/tutorial/first-steps.md b/docs/tutorial/first-steps.md
@@ -671,7 +671,7 @@ good unique identifier.
 === "Command"
 
     ```sh
-    cat code/dcm2bids_config.json
+    cat tmp_dcm2bids/helper/004_In_DCM2NIIX_regression_test_20180918114023.json
     ```
 
 === "Output"
@@ -807,11 +807,11 @@ task name:
       "modalityLabel": "bold",
       "customLabels": "task-rest",
       "criteria": {
-        "SeriesDescription": "Axial EPI-FMRI (Interleaved I to S)*",
-        "sidecarChanges": {
+        "SeriesDescription": "Axial EPI-FMRI (Interleaved I to S)*"
+      },
+      "sidecarChanges": {
         "TaskName": "rest"
       }
-      }
     }
   ]
 }
@@ -887,6 +887,7 @@ file with the appropriate info.
 {
   "descriptions": [
     {
+      "id": "id_task-rest",
       "dataType": "func",
       "modalityLabel": "bold",
       "customLabels": "task-rest",
@@ -904,7 +905,7 @@ file with the appropriate info.
       "criteria": {
         "SeriesDescription": "EPI PE=AP*"
       },
-      "intendedFor": 0
+      "intendedFor": "id_task-rest"
     },
     {
       "dataType": "fmap",
@@ -913,7 +914,7 @@ file with the appropriate info.
       "criteria": {
         "SeriesDescription": "EPI PE=PA*"
       },
-      "intendedFor": 0
+      "intendedFor": "id_task-rest"
     }
   ]
 }

diff --git a/tests/data/config_test.json b/tests/data/config_test.json
@@ -12,6 +12,7 @@
             }
         },
         {
+            "id": "func_task-rest",
             "dataType": "func",
             "modalityLabel": "bold",
             "customLabels": "task-rest",
@@ -21,13 +22,15 @@
             }
         },
         {
+            "id": "T1",
             "dataType": "anat",
             "modalityLabel": "T1w",
             "criteria": {
                 "SidecarFilename": "*MPRAGE*"
             }
         },
         {
+            "id": "id_dwi",
             "dataType": "dwi",
             "modalityLabel": "dwi",
             "criteria": {
@@ -42,7 +45,7 @@
                 "EchoNumber": 1,
                 "EchoTime": 0.00492
             },
-            "intendedFor": [3,2]
+            "intendedFor": ["id_dwi", "T1"]
         },
         {
             "dataType": "fmap",
@@ -53,7 +56,7 @@
                 "EchoTime": 0.00738,
                 "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"]
             },
-            "IntendedFor": 3
+            "IntendedFor": "id_dwi"
         },
         {
             "dataType": "dwi",