BF: split prefix into path (if any) and provide only basename as prefix for dcm2niix invocation

dcm2niix started to segfault whenever -f is too long.
rordenlab/dcm2niix#465

And it feels that we abused -f wherever -o should have been used.
I have not looked though through history of changes if such use of -f
was warranted, but as I see that output_dir is not explicitely defined,
decided to just use that one instead.

this seems to resolve the dcm2niix segfault during
heudiconv/tests/test_heuristics.py::test_scans_keys_reproin
when testing on my laptop

Author: yarikoptic

heudiconv/convert.py

@@ -614,7 +614,11 @@ def nipype_convert(item_dicoms, prefix, with_prov, bids_options, tmpdir, dcmconf
     convertnode = Node(Dcm2niix(from_file=fromfile), name='convert')
     convertnode.base_dir = tmpdir
     convertnode.inputs.source_names = item_dicoms
-    convertnode.inputs.out_filename = prefix
+    convertnode.inputs.out_filename = op.basename(prefix)
+    prefix_dir = op.dirname(prefix)
+    # if provided prefix had a path in it -- pass is as output_dir instead of default curdir
+    if prefix_dir:
+        convertnode.inputs.output_dir = prefix_dir
 
     if nipype.__version__.split('.')[0] == '0':
         # deprecated since 1.0, might be needed(?) before