fix doc, dockers and add skip_dcm2niix

containers/Dockerfile

@@ -12,7 +12,7 @@ RUN apt-get -y install wget build-essential cmake git pigz \
 RUN pip3 install dcm2bids
 
 # Install dcm2niix from github
-ENV DCM2NIIX_VERSION="v1.0.20201102"
+ENV DCM2NIIX_VERSION="v1.0.20230411"
 
 WORKDIR /usr/local/src
 RUN git clone https://github.com/rordenlab/dcm2niix.git

dcm2bids/cli/dcm2bids.py

@@ -64,6 +64,11 @@ def _build_arg_parser():
                    help="Overwrite previous temporary dcm2niix "
                         "output if it exists.")
 
+    p.add_argument("--skip_dcm2niix",
+                   action="store_true",
+                   help="Skip dcm2niix conversion. "
+                        "Option -d should contains NIFTI and json files.")
+
     p.add_argument("--clobber",
                    action="store_true",
                    help="Overwrite output if it exists.")

dcm2bids/dcm2bids_gen.py

@@ -42,6 +42,7 @@ def __init__(
         session=DEFAULT.session,
         clobber=DEFAULT.clobber,
         force_dcm2niix=DEFAULT.force_dcm2niix,
+        skip_dcm2niix=DEFAULT.skip_dcm2niix,
         log_level=DEFAULT.logLevel,
         **_
     ):
@@ -54,6 +55,7 @@ def __init__(
         self.bids_validate = bids_validate
         self.auto_extract_entities = auto_extract_entities
         self.force_dcm2niix = force_dcm2niix
+        self.skip_dcm2niix = skip_dcm2niix
         self.logLevel = log_level
         self.logger = logging.getLogger(__name__)
 
@@ -77,6 +79,7 @@ def run(self):
             self.dicom_dirs,
             self.bids_dir,
             self.participant,
+            self.skip_dcm2niix,
             self.config.get("dcm2niixOptions", DEFAULT.dcm2niixOptions),
         )
 

dcm2bids/dcm2niix_gen.py

@@ -18,6 +18,7 @@ class Dcm2niixGen(object):
         dicom_dirs (list): A list of folder with dicoms to convert
         bids_dir (str): A path to the root BIDS directory
         participant: Optional Participant object
+        skip_dcm2niix: Optional if input only NIFTI and JSON files
         options (str): Optional arguments for dcm2niix
 
     Properties:
@@ -29,6 +30,7 @@ def __init__(
         dicom_dirs,
         bids_dir,
         participant=None,
+        skip_dcm2niix=DEFAULT.skip_dcm2niix,
         options=DEFAULT.dcm2niixOptions,
         helper=False
     ):
@@ -37,6 +39,7 @@ def __init__(
         self.dicom_dirs = dicom_dirs
         self.bids_dir = bids_dir
         self.participant = participant
+        self.skip_dcm2niix = skip_dcm2niix
         self.options = options
         self.helper = helper
 
@@ -96,15 +99,26 @@ def run(self, force=False, helper=False):
     def execute(self):
         """ Execute dcm2niix for each directory in dicom_dirs
         """
-        for dicomDir in self.dicom_dirs:
-            cmd = ['dcm2niix', *shlex.split(self.options),
-                   '-o', self.output_dir, dicomDir]
+        if not self.skip_dcm2niix:
+            for dicomDir in self.dicom_dirs:
+                cmd = ['dcm2niix', *shlex.split(self.options),
+                       '-o', self.output_dir, dicomDir]
+                output = run_shell_command(cmd)
+
+                try:
+                    output = output.decode()
+                except Exception:
+                    pass
+
+                self.logger.debug(f"\n{output}")
+                self.logger.info("Check log file for dcm2niix output\n")
+        else:
+            cmd = ['cp', '-r', dicomDir, self.output_dir]
             output = run_shell_command(cmd)
 
             try:
                 output = output.decode()
             except Exception:
                 pass
-
-            self.logger.debug(f"\n{output}")
-            self.logger.info("Check log file for dcm2niix output\n")
+
+            self.logger.info("Not running dcm2niix\n")

dcm2bids/utils/utils.py

@@ -41,6 +41,7 @@ class DEFAULT(object):
 
     # dcm2niix.py
     dcm2niixOptions = "-b y -ba y -z y -f '%3s_%f_%p_%t'"
+    skip_dcm2niix = False
 
     # sidecar.py
     auto_extractors = {'SeriesDescription': ["task-(?P<task>[a-zA-Z0-9]+)"],

docs/how-to/create-config-file.md

@@ -17,7 +17,7 @@
       }
     },
     {
-      "id": "task-rest",
+      "id": "task_rest",
       "datatype": "func",
       "suffix": "bold",
       "custom_entities": "task-rest",