wip/enh: added bids command line

Author: akeshavan

dmriprep/cli.py

@@ -41,13 +41,13 @@ def main(participant_label, bids_dir, output_dir, analysis_level="participant"):
     if analysis_level is not 'participant':
         raise NotImplementedError('The only valid analysis level for dmriprep is participant at the moment.')
 
-    inputs = io.get_BIDS_files(participant_label, bids_dir)
+    inputs = io.get_bids_files(participant_label, bids_dir)
+
+    for subject_inputs in inputs:
+        run.run_dmriprep_pe(**subject_inputs,
+                            working_dir=os.path.join(output_dir, 'scratch'),
+                            out_dir=output_dir)
 
-    # for subject_id, subject_inputs in inputs:
-    #     run.run_dmriprep_pe(**subject_inputs,
-    #                         working_dir=os.path.join(output_dir, 'scratch'),
-    #                         out_dir=output_dir)
-    click.echo('doing stuff {} {} {} {}'.format(participant_label, bids_dir, output_dir, analysis_level))
     return 0
 
 

dmriprep/io.py

@@ -4,7 +4,72 @@
 """
 from glob import glob
 import os
+import os.path as op
+import bids
 
-def get_BIDS_files(subject_id, bids_input_directory):
+
+def get_bids_subject_input_files(subject_id, bids_input_directory):
+    """
+    Function to return the needed files for dmriprep based on subject id and a bids directory.
+
+    :param subject_id: string
+    :param bids_input_directory: string to bids dir
+    :return: dict of inputs
+    """
+    layout = bids.layout.BIDSLayout(bids_input_directory)
+    subjects = layout.get_subjects()
+    assert subject_id in subjects, "subject {} is not in the bids folder".format(subject_id)
+
+    ap_file = layout.get(subject=subject_id, fmap="epi", modality="fmap", dir="AP")
+    assert len(ap_file) == 1, 'found {} ap fieldmap files and we need just 1'.format(len(ap_file))
+
+    pa_file = layout.get(subject=subject_id, fmap="epi", modality="fmap", dir="PA")
+    assert len(pa_file) == 1, 'found {} pa fieldmap files and we need just 1'.format(len(pa_file))
+
+    dwi_files = layout.get(subject=subject_id, modality="dwi")
+    valid_dwi_files = []
+
+    for d in dwi_files:
+        if d.filename.startswith(op.abspath(op.join(bids_input_directory, 'sub-' + subject_id))):
+            valid_dwi_files.append(d.filename)
+
+    dwi_file = [d for d in valid_dwi_files if d.endswith('.nii.gz') and not "TRACE" in d]
+    assert len(dwi_file) == 1, 'found {} dwi files and we need just 1'.format(len(dwi_file))
+
+    bval_file = [d for d in valid_dwi_files if d.endswith('.bval')]
+    assert len(bval_file) == 1, 'found {} bval files and we need just 1'.format(len(bval_file))
+
+    bvec_file = [d for d in valid_dwi_files if d.endswith('.bvec')]
+    assert len(bvec_file) == 1, 'found {} bvec files and we need just 1'.format(len(bvec_file))
+
+    subjects_dir = op.join(bids_input_directory, 'derivatives', 'sub-'+subject_id)
+
+    if not op.exists(op.join(subjects_dir, 'freesurfer')):
+        raise NotImplementedError('we have not yet implemented a version of dmriprep that runs freesurfer for you.'
+                                  'please run freesurfer and try again'
+                                  )
+
+    outputs = dict(subject_id="sub-"+subject_id,
+                   dwi_file=dwi_file[0],
+                   dwi_file_AP=ap_file[0].filename,
+                   dwi_file_PA=pa_file[0].filename,
+                   bvec_file=bvec_file[0],
+                   bval_file=bval_file[0],
+                   subjects_dir=op.abspath(subjects_dir))
+    return outputs
+
+
+def get_bids_files(subject_id, bids_input_directory):
+    """
+    subject to get all bids files for am optional subject id and bids dir. if subject id is blank then all subjects
+    are used.
+    :param subject_id:
+    :param bids_input_directory:
+    :return:
+    """
     if not subject_id:
-        subjects = glob(os.path.join(bids_input_directory, "*"))
+        subjects = [s.split("/")[-1].replace("sub-", "") for s in glob(os.path.join(bids_input_directory, "sub-*"))]
+        assert len(subjects), "No subject files found in bids directory"
+        return [get_bids_subject_input_files(sub, bids_input_directory) for sub in subjects]
+    else:
+        return [get_bids_subject_input_files(subject_id, bids_input_directory)]

dmriprep/run.py

@@ -227,7 +227,7 @@ def rang(b):
     return dmri_corrected, bvec_rotated, art_file, motion_file, outlier_file
 
 
-def run_dmriprep_pe(dwi_file, dwi_file_AP, dwi_file_PA, bvec_file, bval_file,
+def run_dmriprep_pe(subject_id, dwi_file, dwi_file_AP, dwi_file_PA, bvec_file, bval_file,
                     subjects_dir, working_dir, out_dir):
     """
     This assumes that there are scans with phase-encode directions AP/PA for
@@ -245,7 +245,7 @@ def run_dmriprep_pe(dwi_file, dwi_file_AP, dwi_file_PA, bvec_file, bval_file,
 
     # some bookkeeping (getting the filename, gettings the BIDS subject name)
     dwi_fname = op.split(dwi_file)[1].split(".nii.gz")[0]
-    bids_sub_name = dwi_fname.split("_")[0]
+    bids_sub_name = subject_id
     assert bids_sub_name.startswith("sub-")
 
     # Grab the preprocessing all_fsl_pipeline
@@ -256,10 +256,9 @@ def run_dmriprep_pe(dwi_file, dwi_file_AP, dwi_file_PA, bvec_file, bval_file,
 
     # initialize an overall workflow
     wf = pe.Workflow(name="dmriprep")
-    wf.base_dir = op.abspath(working_dir)
+    wf.base_dir = op.join(op.abspath(working_dir), subject_id)
 
     prep.inputs.inputnode.in_file = dwi_file
-    # prep.inputs.inputnode.alt_file = dwi_file_PA
     prep.inputs.inputnode.in_bvec = bvec_file
     prep.inputs.inputnode.in_bval = bval_file
     eddy = prep.get_node('fsl_eddy')

docker/environment.yml

@@ -5,5 +5,7 @@ dependencies:
    - python=3.6
    - dipy
    - boto3
+   - graphviz
    - pip:
-     - "--editable=git+https://github.com/nipy/nipype@fa0a101fec2d010dcb68910000f66d7c64e5d03e#egg=nipype"
+     - "--editable=git+https://github.com/nipy/nipype@fa0a101fec2d010dcb68910000f66d7c64e5d03e#egg=nipype"
+     - bids