Merge pull request #7 from greydongilmore/patch-1

Create clinicalDBS.py

heuristics/clinicalDBS.py

@@ -0,0 +1,309 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Sat Jun 23 16:14:57 2018
+
+@author: Greydon
+"""
+
+def create_key(template, outtype=('nii.gz'), annotation_classes=None):
+    if template is None or not template:
+        raise ValueError('Template must be a valid format string')
+    return (template, outtype, annotation_classes)
+
+def get_unique(seqinfos, attr):
+    """Given a list of seqinfos, which must have come from a single study
+    get specific attr, which must be unique across all of the entries
+    If not -- fail!
+    """
+    values = set(getattr(si, attr) for si in seqinfos)
+#    assert (len(values) == 1)
+    return values.pop()
+
+def infotoids(seqinfos, outdir):
+
+    subject = get_unique(seqinfos, 'example_dcm_file').split('_')[0]
+    session = get_unique(seqinfos, 'example_dcm_file').split('_')[1]
+
+    ids = {
+    'locator': '',
+    'session': session,
+    'subject': subject,
+    }
+
+    return ids
+
+def infotodict(seqinfo):
+    """Heuristic evaluator for determining which runs belong where
+
+    allowed template fields - follow python string module:
+
+    item: index within category
+    subject: participant id
+    seqitem: run number during scanning
+    subindex: sub index within group
+    """
+
+    #2D TSE 
+    # Transverse
+    fse_tra_T2w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-FSEtra_run-{item:02d}_T2w')
+    pd_tra_T1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-PDtra_run-{item:02d}_T2w')
+    flair_tra_T1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-tra_run-{item:02d}_FLAIR')
+    ssfse_tra_T1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-SSFSEtra_run-{item:02d}_T1w')
+    fse_tra_T2w_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-FSEtraELECTRODE_run-{item:02d}_T2w')
+    pd_tra_T1w_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-PDtraELECTRODE_run-{item:02d}_T2w')
+    flair_tra_T1w_electrode= create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-traELECTRODE_run-{item:02d}_FLAIR')
+
+    #Coronal
+    fse_cor_T2w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-FSEcor_run-{item:02d}_T2w')
+    pd_cor_T1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-PDcor_run-{item:02d}_T2w')
+    flair_cor_T1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-cor_run-{item:02d}_FLAIR')
+    ssfse_cor_T1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-SSFSEcor_run-{item:02d}_T1w')
+    fse_cor_T2w_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-FSEcorELECTRODE_run-{item:02d}_T2w')
+    pd_cor_T1w_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-PDcorELECTRODE_run-{item:02d}_T2w')
+    flair_cor_T1w_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-corELECTRODE_run-{item:02d}_FLAIR')
+
+    #Saggital
+    fse_sag_T2w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-FSEsag_run-{item:02d}_T2w')
+    pd_sag_T1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-PDsag_run-{item:02d}_T2w')
+    flair_sag_T1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-sag_run-{item:02d}_FLAIR')
+    ssfse_sag_T1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-SSFSEsag_run-{item:02d}_T1w')
+
+    #3D Stealth
+    t1 = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-3D_run-{item:02d}_T1w')
+    t1_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-3DELECTRODE_run-{item:02d}_T1w')
+    t2_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-3DELECTRODE_run-{item:02d}_T2w')
+
+    #T2 EPI
+    epi_t2 = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-EPI_run-{item:02d}_T2w')
+    epi_t2_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-EPIELECTRODE_run-{item:02d}_T2w')
+
+    #Localizer
+    loc_tra = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-tra_run-{item:02d}_loc')
+    loc_cor = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-cor_run-{item:02d}_loc')
+    loc_sag = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-sag_run-{item:02d}_loc')
+    loc_3D = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-3D_run-{item:02d}_loc')
+    loc_tra_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-traelectrode_run-{item:02d}_loc')
+    loc_cor_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-corelectrode_run-{item:02d}_loc')
+    loc_sag_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-sagelectrode_run-{item:02d}_loc')
+    loc_3D_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-3Delectrode_run-{item:02d}_loc')
+
+    #MPGR
+    mpgr_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-MPGRELECTRODE_run-{item:02d}_T1w')
+    mpgr_2D = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_mod-2D_acq-MPGR_run-{item:02d}_T1w')
+    mpgr_3D = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_mod-3D_acq-MPGR_run-{item:02d}_T1w')
+
+    #FSPGR
+    fspgr = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-FSPGR_run-{item:02d}_T1w')
+    fspgr_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-FSPGRELECTRODE_run-{item:02d}_T1w')
+
+    #Diffusion
+    trace = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_mod-TRACE_run-{item:02d}_T2w')
+    trace_electrode = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_mod-TRACE_acq-ELECTRODE_run-{item:02d}_T2w')
+
+    #Diffusion
+    dwi = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_run-{item:02d}_dwi')
+    dwi_electrode = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_acq-ELECTRODE_run-{item:02d}_dwi')
+
+    avg_dc = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_mod-AVGDC_run-{item:02d}_T1w')
+    avg_dc_electrode = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_mod-AVGDC_acq-ELECTRODE_run-{item:02d}_T1w')
+
+    fa = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_run-{item:02d}_angio')
+    fa_electrode = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_acq-ELECTRODE_run-{item:02d}_angio')
+
+    #CT
+    ct = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_run-{item:02d}_ct')
+    ct_scout = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-ELECTRODE_run-{item:02d}_ctScout')
+    ct_frame = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_run-{item:02d}_ctFrame')
+    ct_frame_scout = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_run-{item:02d}_ctFrameScout')
+    ct_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-ELECTRODE_run-{item:02d}_ct')
+    ct_scout_electrode = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-ELECTRODE_run-{item:02d}_ctScout')
+
+    #Fluoro Intra
+    xr = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_xr')
+
+    info = {fse_tra_T2w:[],
+            pd_tra_T1w:[],
+            flair_tra_T1w:[],
+            fse_tra_T2w_electrode:[],
+            pd_tra_T1w_electrode:[],
+            flair_tra_T1w_electrode:[],
+            fse_cor_T2w:[],
+            pd_cor_T1w:[],
+            flair_cor_T1w:[],
+            fse_cor_T2w_electrode:[],
+            pd_cor_T1w_electrode:[],
+            flair_cor_T1w_electrode:[],
+            fse_sag_T2w:[],
+            pd_sag_T1w:[],
+            flair_sag_T1w:[],
+            t1:[], 
+            t1_electrode:[],
+            t2_electrode:[],
+            epi_t2:[],
+            epi_t2_electrode:[],
+            loc_tra:[],
+            loc_cor:[],
+            loc_sag:[],
+            loc_3D:[],
+            loc_tra_electrode:[],
+            loc_cor_electrode:[],
+            loc_sag_electrode:[],
+            loc_3D_electrode:[],
+            mpgr_electrode:[],
+            mpgr_2D:[],
+            mpgr_3D:[],
+            fspgr:[],
+            fspgr_electrode:[],
+            ssfse_tra_T1w:[],
+            ssfse_cor_T1w:[],
+            ssfse_sag_T1w:[],
+            trace:[],
+            trace_electrode:[],
+            dwi:[], 
+            dwi_electrode:[],
+            avg_dc:[],
+            avg_dc_electrode:[],
+            fa:[],
+            fa_electrode:[],
+            ct:[],
+            ct_scout:[],
+            ct_frame:[],
+            ct_frame_scout:[],
+            ct_electrode:[],
+            ct_scout_electrode:[],
+            xr:[]}
+
+    for idx, s in enumerate(seqinfo):
+        if any(substring in s.study_description.upper() for substring in {'MR'}):
+
+            if any(substring in s.series_description.upper() for substring in {'STEALTH','3D','STEREO'}):
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name:
+                    if 'T2' in s.series_description.upper():
+                        info[t2_electrode].append({'item': s.series_id})
+                    else:
+                        info[t1_electrode].append({'item': s.series_id})
+                else:
+                    info[t1].append({'item': s.series_id})
+
+            if 'EPI' in s.series_description.upper():
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name:
+                    info[epi_t2_electrode].append({'item': s.series_id})
+                elif 'T2' in s.series_description.upper():
+                    info[epi_t2].append({'item': s.series_id})
+
+            if 'MPGR' in s.series_description.upper():
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name:
+                    info[mpgr_electrode].append({'item': s.series_id})
+                elif 'AX' in s.series_description.upper():
+                    info[mpgr_2D].append({'item': s.series_id})
+                else:
+                    info[mpgr_3D].append({'item': s.series_id})
+
+            if any(substring in s.series_description.upper() for substring in {'IR_FSPGR','FSPGR'}):
+                if not any(substring in s.series_description.upper() for substring in {'STEALTH','3D','STEREO'}):
+                    if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name.upper():
+                        info[fspgr_electrode].append({'item': s.series_id})
+                    else:
+                        info[fspgr].append({'item': s.series_id})
+
+            if 'AX' in s.series_description.upper() and '3D' not in s.series_description.upper():
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name.upper():
+                    if any(substring in s.series_description.upper() for substring in {'T2','2D'}):
+                        info[fse_tra_T2w_electrode].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'PD'}):
+                        info[pd_tra_T1w_electrode].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'FLAIR'}):
+                        info[flair_tra_T1w_electrode].append({'item': s.series_id})
+                else:
+                    if any(substring in s.series_description.upper() for substring in {'T2','2D'}):
+                        info[fse_tra_T2w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'PD'}):
+                        info[pd_tra_T1w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'FLAIR'}):
+                        info[flair_tra_T1w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'SSFSE'}):
+                        info[ssfse_tra_T1w].append({'item': s.series_id})
+
+            if 'COR' in s.series_description.upper() and '3D' not in s.series_description.upper():
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name.upper():
+                    if any(substring in s.series_description.upper() for substring in {'T2','2D'}):
+                        info[fse_cor_T2w_electrode].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'PD'}):
+                        info[pd_cor_T1w_electrode].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'FLAIR'}):
+                        info[flair_cor_T1w_electrode].append({'item': s.series_id})
+                else:
+                    if any(substring in s.series_description.upper() for substring in {'T2','2D'}):
+                        info[fse_cor_T2w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'PD'}):
+                        info[pd_cor_T1w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'FLAIR'}):
+                        info[flair_cor_T1w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'SSFSE'}):
+                        info[ssfse_cor_T1w].append({'item': s.series_id})
+
+            if 'SAG' in s.series_description.upper() and '3D' not in s.series_description.upper():
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name.upper():
+                    if any(substring in s.series_description.upper() for substring in {'T2','2D'}):
+                        info[fse_sag_T2w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'PD'}):
+                        info[pd_sag_T1w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'FLAIR'}):
+                        info[flair_sag_T1w].append({'item': s.series_id})
+                else:
+                    if any(substring in s.series_description.upper() for substring in {'T2','2D'}):
+                        info[fse_sag_T2w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'PD'}):
+                        info[pd_sag_T1w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'FLAIR'}):
+                        info[flair_sag_T1w].append({'item': s.series_id})
+                    elif any(substring in s.series_description.upper() for substring in {'SSFSE'}):
+                            info[ssfse_cor_T1w].append({'item': s.series_id})
+
+            if any(substring in s.series_description.upper() for substring in {'DWI','DIFFUSION'}):
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name.upper():
+                    info[dwi_electrode].append({'item': s.series_id})
+                else:
+                    info[dwi].append({'item': s.series_id})
+
+            if 'TRACE' in s.series_description.upper():
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name.upper():
+                    info[trace_electrode].append({'item': s.series_id})
+                else:
+                    info[trace].append({'item': s.series_id})
+
+            if any(substring in s.series_description.upper() for substring in {'DC','AVERAGE'}):
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name.upper():
+                    info[avg_dc_electrode].append({'item': s.series_id})
+                else:
+                    info[avg_dc].append({'item': s.series_id})
+
+            if any(substring in s.series_description.upper() for substring in {'FRACTIONAL','ANSIO','ANSIO.'}):
+                if 'SAR' in s.series_description.upper() or 'SAFE' in s.protocol_name.upper():
+                    info[fa_electrode].append({'item': s.series_id})
+                else:
+                    info[fa].append({'item': s.series_id})
+
+        #   CT SCANS 
+        elif any(substring in s.study_description.upper() for substring in {'CT','HEAD'}):
+            electrode_list = {'OVER','UNDER', 'ELECTRODE','ROUTINE','F_U_HEAD','F/U_HEAD', 'ER_HEAD'}
+            frame_list     = {'STEROTACTIC','STEREOTACTIC','STEALTH','CTA_COW'}
+
+            if any(substring in s.protocol_name.upper() for substring in electrode_list):
+                if 'SCOUT' not in s.series_description.upper():
+                    info[ct_electrode].append({'item': s.series_id})
+            elif any(substring in s.protocol_name.upper() for substring in frame_list):
+                if 'SCOUT' not in s.series_description.upper():
+                    info[ct_frame].append({'item': s.series_id})
+            else:
+                if 'SCOUT' not in s.series_description.upper():
+                    info[ct].append({'item': s.series_id})
+
+        # INTRAOP X-RAY 
+        elif any(substring in s.study_description.upper() for substring in {'INTRAOPERATIVE','SKULL','OT','XA','RF'}):
+            if 'CR' not in s.study_description.upper():
+                info[xr].append({'item': s.series_id})
+        elif any(substring.upper() in s.image_type for substring in {'SINGLE PLANE'}):
+                info[xr].append({'item': s.series_id})
+
+    return info