Add option to skip_dcm2niix and reorganize NIFTI and JSON files

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 +99,23 @@ 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]
-            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")
+        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:
+            for dicomDir in self.dicom_dirs:
+                shutil.copytree(dicomDir, self.output_dir, dirs_exist_ok=True)
+                cmd = ['cp', '-r', dicomDir, self.output_dir]
+                self.logger.info("Running: %s", " ".join(str(item) for item in cmd))
+
+            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/get-started/install.md

@@ -344,8 +344,8 @@ dcm2bids command such as `dcm2bids --help`:
 ```bash hl_lines="1"
 (dcm2bids) sam:~/dcm2bids-proj$ dcm2bids --help
 usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c
-                CONFIG [-o OUTPUT_DIR] [--forceDcm2niix] [--clobber]
-                [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
+                CONFIG [-o OUTPUT_DIR] [--force_dcm2niix] [--skip_dcm2niix]
+                [--clobber] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
 
 Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
 dcm2bids 2.1.7
@@ -363,7 +363,8 @@ options:
   -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                         Output BIDS directory, Default: current directory
                         (/home/sam/dcm2bids-proj)
-  --forceDcm2niix       Overwrite previous temporary dcm2niix output if it exists
+  --force_dcm2niix       Overwrite previous temporary dcm2niix output if it exists
+  --skip_dcm2niix       Skip dcm2niix conversion. Option -d should contains NIFTI and json files.
   --clobber             Overwrite output if it exists
   -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                         Set logging level

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",

docs/how-to/use-advanced-commands.md

@@ -216,7 +216,7 @@ command.
     ```sh hl_lines="2-3"
     (dcm2bids) sam:~/dcm2bids-tutorial/bids_project$ dcm2bids --help
     usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c CONFIG [-o OUTPUT_DIR]
-                    [--auto_extract_entities] [--bids_validate] [--forceDcm2niix] [--clobber]
+                    [--auto_extract_entities] [--bids_validate] [--force_dcm2niix] [--skip_dcm2niix] [--clobber]
                     [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
 
     Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
@@ -238,8 +238,9 @@ command.
                             depending on the suffix and datatype. [False]
     --bids_validate       If set, once your conversion is done it will check if your output folder is BIDS valid. [False]
                           bids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart
-    --force_dcm2niix       Overwrite previous temporary dcm2niix output if it exists
-    --clobber             Overwrite output if it exists
+    --force_dcm2niix       Overwrite previous temporary dcm2niix output if it exists.
+    --skip_dcm2niix       Skip dcm2niix conversion. Option -d should contains NIFTI and json files.
+    --clobber             Overwrite output if it exists.
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                             Set logging level
 
@@ -318,3 +319,8 @@ By default, dcm2bids will not validate your final BIDS structure. If needed, you
 can install
 [bids-validator](https://github.com/bids-standard/bids-validator#quickstart) and
 activate this option.
+
+### `--skip_dcm2niix`
+
+If you don't have access to original dicom files you can still use dcm2bids to reorganise your data into a BIDS structure.
+Using the option --skip_dcm2niix you will skip the conversion step.

docs/tutorial/first-steps.md

@@ -81,7 +81,7 @@ You can test it with any command but a safe way is to use the `--help` command.
     (dcm2bids) sam:~$ dcm2bids --help
     usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c
                     CONFIG [-o OUTPUT_DIR][--auto_extract_entities] [--bids_validate]
-                    [--forceDcm2niix] [--clobber]
+                    [--force_dcm2niix] [--skip_dcm2niix] [--clobber]
                     [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
 
     Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
@@ -104,8 +104,9 @@ You can test it with any command but a safe way is to use the `--help` command.
                           If set, it will automatically try to extract entityinformation [task, dir, echo] based on the suffix and datatype. [False]
     --bids_validate       If set, once your conversion is done it will check if your output folder is BIDS valid. [False]
                           bids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart
-    --forceDcm2niix       Overwrite previous temporary dcm2niix output if it exists
-    --clobber             Overwrite output if it exists
+    --force_dcm2niix       Overwrite previous temporary dcm2niix output if it exists.
+    --skip_dcm2niix       Skip dcm2niix conversion. Option -d should contains NIFTI and json files.
+    --clobber             Overwrite output if it exists.
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                             Set logging level
     -a, --anonymizer      This option no longer exists from the script in this
@@ -1069,7 +1070,7 @@ command.
     ```sh hl_lines="2-3"
     (dcm2bids) sam:~/dcm2bids-tutorial/bids_project$ dcm2bids --help
     usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c CONFIG [-o OUTPUT_DIR]
-                    [--auto_extract_entities] [--bids_validate] [--forceDcm2niix] [--clobber]
+                    [--auto_extract_entities] [--bids_validate] [--force_dcm2niix] [--skip_dcm2niix] [--clobber]
                     [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-a]
 
     Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure
@@ -1091,9 +1092,9 @@ command.
                             If set, it will automatically try to extract entityinformation [task, dir, echo] based on the suffix and datatype. [False]
     --bids_validate         If set, once your conversion is done it will check if your output folder is BIDS valid. [False]
                             bids-validator needs to be installed check: https://github.com/bids-standard/bids-validator#quickstart
-
-    --forceDcm2niix       Overwrite previous temporary dcm2niix output if it exists
-    --clobber             Overwrite output if it exists
+    --force_dcm2niix       Overwrite previous temporary dcm2niix output if it exists.
+    --skip_dcm2niix       Skip dcm2niix conversion. Option -d should contains NIFTI and json files.
+    --clobber             Overwrite output if it exists.
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                             Set logging level
     -a, --anonymizer      This option no longer exists from the script in this release. See:https://github.com/unfmontreal/Dcm2Bids/blob/master/README.md#defaceTpl