Merge pull request #248 from UNFmontreal/add_option_for_nifti_only

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

@@ -59,10 +59,15 @@ def _build_arg_parser():
                         "\nbids-validator needs to be installed check: "
                         f"{DEFAULT.link_bids_validator}")
 
-    p.add_argument("--force_dcm2niix",
+    p.add_argument("--force_dcm2bids",
                    action="store_true",
-                   help="Overwrite previous temporary dcm2niix "
-                        "output if it exists.")
+                   help="Overwrite previous temporary dcm2bids "
+                         "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",

dcm2bids/cli/dcm2bids_helper.py

@@ -41,7 +41,7 @@ def _build_arg_parser():
                         "Defaults to DICOM_DIR if no name is provided.\n"
                         "(Default: [%(default)s])")
 
-    p.add_argument('--force', '--force_dcm2niix',
+    p.add_argument('--force', '--force_dcm2bids',
                    dest='overwrite', action='store_true',
                    help='Force command to overwrite existing output files.')
 

dcm2bids/dcm2bids_gen.py

@@ -26,8 +26,8 @@ class Dcm2BidsGen(object):
         output_dir (path): Path to the BIDS base folder
         session (str): Optional label of a session
         clobber (boolean): Overwrite file if already in BIDS folder
-        force_dcm2niix (boolean): Forces a cleaning of a previous execution of
-                                 dcm2niix
+        force_dcm2bids (boolean): Forces a cleaning of a previous execution of
+                                 dcm2bids
         log_level (str): logging level
     """
 
@@ -41,7 +41,8 @@ def __init__(
         auto_extract_entities=False,
         session=DEFAULT.session,
         clobber=DEFAULT.clobber,
-        force_dcm2niix=DEFAULT.force_dcm2niix,
+        force_dcm2bids=DEFAULT.force_dcm2bids,
+        skip_dcm2niix=DEFAULT.skip_dcm2niix,
         log_level=DEFAULT.logLevel,
         **_
     ):
@@ -53,7 +54,8 @@ def __init__(
         self.clobber = clobber
         self.bids_validate = bids_validate
         self.auto_extract_entities = auto_extract_entities
-        self.force_dcm2niix = force_dcm2niix
+        self.force_dcm2bids = force_dcm2bids
+        self.skip_dcm2niix = skip_dcm2niix
         self.logLevel = log_level
         self.logger = logging.getLogger(__name__)
 
@@ -77,10 +79,11 @@ def run(self):
             self.dicom_dirs,
             self.bids_dir,
             self.participant,
+            self.skip_dcm2niix,
             self.config.get("dcm2niixOptions", DEFAULT.dcm2niixOptions),
         )
 
-        dcm2niix.run(self.force_dcm2niix)
+        dcm2niix.run(self.force_dcm2bids)
 
         sidecars = []
         for filename in dcm2niix.sidecarFiles:

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
 
@@ -52,7 +55,7 @@ def output_dir(self):
             tmpDir = self.bids_dir
         return tmpDir
 
-    def run(self, force=False, helper=False):
+    def run(self, force=False):
         """ Run dcm2niix if necessary
 
         Args:
@@ -68,10 +71,10 @@ def run(self, force=False, helper=False):
             oldOutput = False
 
         if oldOutput and force:
-            self.logger.warning("Previous dcm2niix directory output found:")
+            self.logger.warning("Previous dcm2bids temporary directory output found:")
             self.logger.warning(self.output_dir)
             self.logger.warning("'force' argument is set to True")
-            self.logger.warning("Cleaning the previous directory and running dcm2niix")
+            self.logger.warning("Cleaning the previous directory and running dcm2bids")
 
             shutil.rmtree(self.output_dir, ignore_errors=True)
 
@@ -81,9 +84,9 @@ def run(self, force=False, helper=False):
             self.execute()
 
         elif oldOutput:
-            self.logger.warning("Previous dcm2niix directory output found:")
+            self.logger.warning("Previous dcm2bids temporary directory output found:")
             self.logger.warning(self.output_dir)
-            self.logger.warning("Use --force_dcm2niix to rerun dcm2niix\n")
+            self.logger.warning("Use --force_dcm2bids to rerun dcm2bids\n")
 
         else:
             if not os.path.exists(self.output_dir):
@@ -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

@@ -26,7 +26,7 @@ class DEFAULT(object):
     bids_validate = False
     auto_extract_entities = False
     clobber = False
-    force_dcm2niix = False
+    force_dcm2bids = False
     post_op = []
     logLevel = "WARNING"
 
@@ -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_dcm2bids] [--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_dcm2bids       Overwrite previous temporary dcm2bids 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_dcm2bids] [--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_dcm2bids       Overwrite previous temporary dcm2bids 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_dcm2bids] [--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_dcm2bids       Overwrite previous temporary dcm2bids 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
@@ -501,7 +502,7 @@ As usual the first command will be to request the help info.
                             to make a config file due to slight variations in MRI acquisitions.
                             Defaults to DICOM_DIR if no name is provided.
                             (Default: [False])
-    --force, --force_dcm2niix
+    --force, --force_dcm2bids
                             Force command to overwrite existing output files.
     -l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                             Set logging level to the console. [INFO]
@@ -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_dcm2bids] [--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_dcm2bids       Overwrite previous temporary dcm2bids 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