Merge pull request #208 from mgxd/enh/dcm2niix-opts

enh: allow additional dcm2niix configuration

Author: mgxd

heudiconv/cli/run.py

@@ -212,6 +212,8 @@ def get_parser():
                         'jsons')
     parser.add_argument('--random-seed', type=int, default=None,
                         help='Random seed to initialize RNG')
+    parser.add_argument('--dcmconfig', default=None,
+                        help='JSON file for additional dcm2niix configuration')
     submission = parser.add_argument_group('Conversion submission options')
     submission.add_argument('-q', '--queue', default=None,
                             help='select batch system to submit jobs to instead'
@@ -231,14 +233,12 @@ def process_args(args):
 
     outdir = op.abspath(args.outdir)
 
-    if args.command:
-        process_extra_commands(outdir, args)
-        return
-
     lgr.info(INIT_MSG(packname=__packagename__,
                       version=__version__))
 
-
+    if args.command:
+        process_extra_commands(outdir, args)
+        return
     #
     # Load heuristic -- better do it asap to make sure it loads correctly
     #
@@ -335,7 +335,8 @@ def process_args(args):
                         bids=args.bids,
                         seqinfo=seqinfo,
                         min_meta=args.minmeta,
-                        overwrite=args.overwrite,)
+                        overwrite=args.overwrite,
+                        dcmconfig=args.dcmconfig,)
 
         lgr.info("PROCESSING DONE: {0}".format(
             str(dict(subject=sid, outdir=study_outdir, session=session))))

heudiconv/convert.py

@@ -79,7 +79,7 @@ def conversion_info(subject, outdir, info, filegroup, ses):
 
 def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
                    anon_outdir, with_prov, ses, bids, seqinfo, min_meta,
-                   overwrite):
+                   overwrite, dcmconfig):
     if dicoms:
         lgr.info("Processing %d dicoms", len(dicoms))
     elif seqinfo:
@@ -194,7 +194,8 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
                 bids=bids,
                 outdir=tdir,
                 min_meta=min_meta,
-                overwrite=overwrite,)
+                overwrite=overwrite,
+                dcmconfig=dcmconfig,)
 
     for item_dicoms in filegroup.values():
         clear_temp_dicoms(item_dicoms)
@@ -211,7 +212,8 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
 
 
 def convert(items, converter, scaninfo_suffix, custom_callable, with_prov,
-            bids, outdir, min_meta, overwrite, symlink=True, prov_file=None):
+            bids, outdir, min_meta, overwrite, symlink=True, prov_file=None,
+            dcmconfig=None):
     """Perform actual conversion (calls to converter etc) given info from
     heuristic's `infotodict`
 
@@ -278,7 +280,7 @@ def convert(items, converter, scaninfo_suffix, custom_callable, with_prov,
 
                     # run conversion through nipype
                     res, prov_file = nipype_convert(item_dicoms, prefix, with_prov,
-                                                    bids, tmpdir)
+                                                    bids, tmpdir, dcmconfig)
 
                     bids_outfiles = save_converted_files(res, item_dicoms, bids,
                                                          outtype, prefix,
@@ -382,8 +384,25 @@ def convert_dicom(item_dicoms, bids, prefix,
                 shutil.copyfile(filename, outfile)
 
 
-def nipype_convert(item_dicoms, prefix, with_prov, bids, tmpdir):
-    """ """
+def nipype_convert(item_dicoms, prefix, with_prov, bids, tmpdir, dcmconfig=None):
+    """
+    Converts DICOMs grouped from heuristic using Nipype's Dcm2niix interface.
+
+    Parameters
+    ----------
+    item_dicoms : List
+        DICOM files to convert
+    prefix : String
+        Heuristic output path
+    with_prov : Bool
+        Store provenance information
+    bids : Bool
+        Output BIDS sidecar JSONs
+    tmpdir : Directory
+        Conversion working directory
+    dcmconfig : File (optional)
+        JSON file used for additional Dcm2niix configuration
+    """
     import nipype
     if with_prov:
         from nipype import config
@@ -393,9 +412,11 @@ def nipype_convert(item_dicoms, prefix, with_prov, bids, tmpdir):
 
     item_dicoms = list(map(op.abspath, item_dicoms)) # absolute paths
 
-    dicom_dir = op.dirname(item_dicoms[0]) if item_dicoms else None
+    fromfile = dcmconfig if dcmconfig else None
+    if fromfile:
+        lgr.info("Using custom config file %s", fromfile)
 
-    convertnode = Node(Dcm2niix(), name='convert')
+    convertnode = Node(Dcm2niix(from_file=fromfile), name='convert')
     convertnode.base_dir = tmpdir
     convertnode.inputs.source_names = item_dicoms
     convertnode.inputs.out_filename = op.basename(op.dirname(prefix))