Fixing small bugs

bip/main.py

@@ -45,15 +45,15 @@ class Context(Config):
         env = {'BIPDIR' : bip.BIPDIR,
                'FSLDIR' : os.environ['FSLDIR']}
 
+        self.subject = subject
+        self.BIPDIR  = env['BIPDIR']
+        self.FSLDIR  = env['FSLDIR']
+
         if not cfgdir:
             cfgdir = self.get_data('config/config.toml')
 
         Config.__init__(self, cfgdir=cfgdir, env=env)
 
-        self.subject = subject
-        self.BIPDIR  = env['BIPDIR']
-        self.FSLDIR  = env['FSLDIR']
-
         with open(self.get_data('dMRI/autoptx/struct_list.json'), 'r',
                   encoding="utf-8") as f:
             self.tract_struct = json.load(f)
@@ -66,18 +66,20 @@ class Context(Config):
     def MNI_brain_mask(self):
         return self.get_standard('MNI152_T1_1mm_brain_mask')
 
-    def get_standard(self, fileName):
-        fileName.replace('/', os.sep)
+    def get_standard(self, file_name):
+        file_name = file_name.replace('/', os.sep)
         basedir = self.FSLDIR + os.sep + op.join('data', 'standard') + os.sep
-        return basedir + fileName
+        return basedir + file_name
 
-    def get_atlas(self, fileName):
-        fileName.replace('/', os.sep)
+    def get_atlas(self, file_name):
+        file_name = file_name.replace('/', os.sep)
         basedir = self.FSLDIR + os.sep + op.join('data', 'atlases') + os.sep
-        return basedir + fileName
+        return basedir + file_name
 
-    def get_data(self, fileName):
-        return bip.utils.get_data(fileName)
+    @staticmethod
+    def get_data(file_name):
+        file_name = file_name.replace('/', os.sep)
+        return bip.utils.get_data(file_name)
 
 
 def parseArguments():
@@ -87,7 +89,10 @@ def parseArguments():
     #########################
     parser = MyParser(description='BioBank Pipeline Manager V. 2.0')
     parser.add_argument("subjectFolder", help='Subject Folder', action="store")
-    parser.add_argument("configDir", help='configDir', action="store")
+    parser.add_argument("-c", "--configDir",
+                        help='Configuration folder: '+
+                             'A config.toml file must exist.',
+                        action="store", default=bip.utils.get_data('config'))
 
     return parser.parse_args()
 

bip/pipelines/dMRI_diff/diff_autoptx.py

@@ -51,7 +51,8 @@ def run(ctx,
         seed_mult = ctx.get('dMRI_multiplier_autoPtx_seeds', 300)
         t_seeds = int(ctx.tract_struct[t_name]["num_seeds"] * seed_mult)
 
-        orig_tract_dir = ctx.get_data('dMRI/autoptx/protocols/' + t_name + '/')
+        orig_tract_dir = ctx.get_data('dMRI/autoptx/protocols/' + t_name) + \
+                         op.sep
         FMRIB58_FA_1mm = ctx.get_standard('FMRIB58_FA_1mm.nii.gz')
 
         # Does the protocol defines a second

bip/pipelines/dMRI_diff/diff_tbss.py

@@ -139,7 +139,7 @@ def run(ctx,
         wrappers.fslmaths(TBSS_all_FA).mas(TBSS_mean_FA_skeleton_mask).\
             run(TBSS_all_FA_skeletonised)
 
-        atlas = ctx.get_data('/dMRI/TBSS/JHU-ICBM-labels-1mm.nii.gz')
+        atlas = ctx.get_data('dMRI/TBSS/JHU-ICBM-labels-1mm.nii.gz')
         mean = wrappers.fslstats(TBSS_all_FA_skeletonised, K=atlas).M.run()
 
         # TODO: Funnily enough, this atlas has changed over time, so for v2

bip/pipelines/fMRI_rest/rfMRI_netmats.py

@@ -35,7 +35,7 @@ def run(ctx,
     with redirect_logging(job_name(run, D), outdir=logs_dir):
 
         MNI_2mm_mask = ctx.get_standard("MNI152_T1_2mm_brain_mask.nii.gz")
-        group_IC = ctx.get_data("/netmats/melodic_IC_" + D + ".nii.gz")
+        group_IC = ctx.get_data("netmats/melodic_IC_" + D + ".nii.gz")
 
         # Create this directory in case it does not exist. This may
         # happen due to the overwrite function issue in Melodic

bip/pipelines/struct_FS/FS_get_IDPs.py

@@ -10,6 +10,8 @@
 # pylint: disable=W0613,R1718,C0201,C0206,R0912,W0702,C0301
 #
 
+import os
+import os.path as op
 import logging
 from pipe_tree import In, Out, Ref
 from bip.pipelines.struct_FS.FS_get_IDPs_fnc import bb_FS_get_IDPs
@@ -20,8 +22,15 @@ log = logging.getLogger(__name__)
 def run(ctx,
         ThalamicNuclei:             In,
         rh_entorhinal_exvivo_label: In,
+        FS_stats_dir:               In,
+        FreeSurfer_dir:             In,
         logs_dir:                   Ref,
-        FS_IDPs:                    Out):
+        FS_IDPs:                    Out,
+        FS_headers_info:            Out):
 
     with redirect_logging(job_name(run), outdir=logs_dir):
-        bb_FS_get_IDPs(ctx)
+
+        env = dict(os.environ, SUBJECTS_DIR=op.join(os.getcwd(), ctx.subject))
+
+        bb_FS_get_IDPs(ctx, env, FreeSurfer_dir, FS_IDPs, FS_headers_info,
+                       FS_stats_dir)

bip/pipelines/struct_FS/FS_get_IDPs_fnc.py

@@ -31,82 +31,89 @@ def read_file(fileName):
             result.append([x.replace("\n", '') for x in line.split(' ')])
     return result
 
-
-def generate_FS_IDP_files(subjects_dir, subject_ID, subject, dataDir,
-                          headersDir, ctx):
-
-    statsDir = op.join(subjects_dir, subject_ID, 'stats') + os.sep
+def generate_FS_IDP_files(subject_ID, FS_stats_dir, data_dir, ctx, env):
 
     # ODO: Include a pre-requisite that python2.7 must be availble in the system
-    if op.isfile(statsDir + 'aseg.stats'):
+    if op.isfile(op.join(FS_stats_dir, 'aseg.stats')):
         run_command(log, 'asegstats2table  ' +
-                         ' -m volume --all-segs --tablefile ' + dataDir +
-                         'aseg_1.txt --subjects ' + subject_ID + ' --skip')
+                         ' -m volume --all-segs --tablefile ' +
+                         op.join(data_dir, 'aseg_1.txt') +
+                         ' --subjects ' + subject_ID +
+                         ' --skip', env=env)
         run_command(log, 'asegstats2table  ' +
-                         ' -m mean --all-segs --tablefile ' + dataDir +
-                         'aseg_intensity.txt ' + ' --subjects ' + subject_ID +
-                         ' --skip')
+                         ' -m mean --all-segs --tablefile ' +
+                         op.join(data_dir, 'aseg_intensity.txt') +
+                         ' --subjects ' + subject_ID +
+                         ' --skip', env=env)
 
-    if op.isfile(statsDir + 'lh.w-g.pct.stats'):
+    if op.isfile(op.join(FS_stats_dir, 'lh.w-g.pct.stats')):
         run_command(log, 'asegstats2table ' +
                          ' -m mean --all-segs --stats=lh.w-g.pct.stats ' +
-                         ' --tablefile ' + dataDir + 'wg_lh_mean.txt ' +
-                         ' --subjects ' + subject_ID + ' --skip')
+                         ' --tablefile ' +
+                         op.join(data_dir, 'wg_lh_mean.txt ') +
+                         ' --subjects ' + subject_ID +
+                         ' --skip', env=env)
 
-    if op.isfile(statsDir + 'rh.w-g.pct.stats'):
+    if op.isfile(op.join(FS_stats_dir, 'rh.w-g.pct.stats')):
         run_command(log, 'asegstats2table ' +
                          ' -m mean --all-segs --stats=rh.w-g.pct.stats ' +
-                         ' --tablefile ' + dataDir + 'wg_rh_mean.txt ' +
-                         ' --subjects ' + subject_ID + ' --skip')
+                         ' --tablefile ' +
+                         op.join(data_dir, 'wg_rh_mean.txt ') +
+                         ' --subjects ' + subject_ID +
+                         ' --skip', env=env)
 
     for hemi in ["lh", "rh"]:
         for value in ["volume", "area", "thickness"]:
             for atlas in ["BA_exvivo", "aparc.DKTatlas", "aparc.a2009s",
                           "aparc"]:
-                outFileName = dataDir + atlas + '_' + hemi + '_' + value +\
-                              '.txt'
-                if op.isfile(statsDir + hemi + "." + atlas + '.stats'):
+                file_name = atlas + '_' + hemi + '_' + value + '.txt'
+                out_file_name = op.join(data_dir, file_name)
+                if op.isfile(op.join(FS_stats_dir,
+                                     hemi + "." + atlas + '.stats')):
                     run_command(log, 'aparcstats2table ' +
                                      ' -m ' + value + ' --hemi=' + hemi +
-                                     ' --tablefile ' + outFileName +
+                                     ' --tablefile ' + out_file_name +
                                      ' --subjects ' + subject_ID +
-                                     ' --skip -p ' + atlas)
+                                     ' --skip -p ' + atlas, env=env)
 
     atlas = "aparc.pial"
     value = "area"
     for hemi in ["lh", "rh"]:
-        outFileName = dataDir + atlas + '_' + hemi + '_' + value + '.txt'
-        if op.isfile(statsDir + hemi + '.aparc.pial.stats'):
+        file_name = atlas + '_' + hemi + '_' + value + '.txt'
+        out_file_name = op.join(data_dir, file_name)
+        if op.isfile(op.join(FS_stats_dir, hemi + '.aparc.pial.stats')):
             run_command(log, 'aparcstats2table ' +
                              ' -m ' + value + ' --hemi=' + hemi +
-                             ' --tablefile ' + outFileName +
+                             ' --tablefile ' + out_file_name +
                              ' --subjects ' + subject_ID +
-                             ' --skip -p ' + atlas)
+                             ' --skip -p ' + atlas, env=env)
 
     with open(ctx.get_data('FS/FS_initial_files.txt'), encoding="utf-8") as f:
-        files_generated = [x.replace('\n', '').split(" ") for x in f.readlines()]
+        files_generated = [x.replace('\n', '').split(" ")
+                           for x in f.readlines()]
 
     data_dict = {}
 
     for file_generated in files_generated:
-        if op.isfile(dataDir + file_generated[0] + '.txt'):
-            data = read_file(dataDir + file_generated[0] + '.txt')
+        file_name = op.join(data_dir, file_generated[0] + '.txt')
+        if op.isfile(file_name):
+            data = read_file(file_name)
         else:
             data = read_file(ctx.get_data('FS/FS_data_ex/' +
                                           file_generated[0] + '.txt'))
         data_dict[file_generated[0]] = data
 
-    data_dict['ID'] = [['ID'], [subject]]
+    data_dict['ID'] = [['ID'], [ctx.subject]]
 
     return data_dict
 
 
 # Quick consistency check
-def check_consistency(data_dict, subjects_dir, ctx):
+def check_consistency(data_dict, subjects_dir, FS_IDPs, ctx):
 
     for file_generated in data_dict.keys():
         if len(data_dict[file_generated]) > 2:
-            save_data_NaNs(subjects_dir, ctx)
+            save_data_NaNs(subjects_dir, FS_IDPs, ctx)
             raise Exception("Error in " + file_generated +
                             ': File has more than 2 lines')
 
@@ -114,45 +121,49 @@ def check_consistency(data_dict, subjects_dir, ctx):
         len1 = len(data_dict[file_generated][1])
 
         if len0 != len1:
-            save_data_NaNs(subjects_dir, ctx)
+            save_data_NaNs(subjects_dir, FS_IDPs, ctx)
             raise Exception("Error in " + file_generated +
                             ': Inconsistent # of features')
 
 
 def fix_aseg_data(data_dict, subjectDir):
 
+    s_1 = 'aseg_1'
+    s_global = 'aseg_global'
+
     # Split aseg_1 into aseg_global and aseg_volume
-    data_dict['aseg_global'] = [[], []]
-    data_dict['aseg_global'][0] = [data_dict['aseg_1'][0][0]] + data_dict['aseg_1'][0][46:]
-    data_dict['aseg_global'][1] = [data_dict['aseg_1'][1][0]] + data_dict['aseg_1'][1][46:]
+    data_dict[s_global] = [[], []]
+    data_dict[s_global][0] = [data_dict[s_1][0][0]] + data_dict[s_1][0][46:]
+    data_dict[s_global][1] = [data_dict[s_1][1][0]] + data_dict[s_1][1][46:]
 
     # Variables not needed
     vars_to_delete = ['CortexVol', 'CerebralWhiteMatterVol',
                       'SupraTentorialVolNotVentVox', 'MaskVol', 'SurfaceHoles']
     ind_to_delete = []
-    for i in range(len(data_dict['aseg_global'][0])):
-        if not data_dict['aseg_global'][0][i] in vars_to_delete:
+    for i in range(len(data_dict[s_global][0])):
+        if not data_dict[s_global][0][i] in vars_to_delete:
             ind_to_delete.append(i)
 
-    data_dict['aseg_global'][0] = [data_dict['aseg_global'][0][x] for x in ind_to_delete]
-    data_dict['aseg_global'][1] = [data_dict['aseg_global'][1][x] for x in ind_to_delete]
+    data_dict[s_1][0] = [data_dict[s_1][0][x] for x in ind_to_delete]
+    data_dict[s_1][1] = [data_dict[s_1][1][x] for x in ind_to_delete]
 
     # For some reason, the VentricleChoroidVol is not caught by asegstats2table
     try:
         file_name = op.join(subjectDir, 'stats' , 'aseg.stats')
         with open(file_name, 'r', encoding="utf-8") as f:
-            val = [x.split(',')[3].strip() for x in f.readlines() if 'VentricleChoroidVol' in x]
+            val = [x.split(',')[3].strip() for x in f.readlines()
+                   if 'VentricleChoroidVol' in x]
     except Exception:
         val = ["NaN"]
 
-    data_dict['aseg_global'][0].append('VentricleChoroidVol')
-    data_dict['aseg_global'][1].append(val[0])
+    data_dict[s_global][0].append('VentricleChoroidVol')
+    data_dict[s_global][1].append(val[0])
 
-    data_dict['aseg_volume'] = [[], []]
-    data_dict['aseg_volume'][0] = data_dict['aseg_1'][0][0:46]
-    data_dict['aseg_volume'][1] = data_dict['aseg_1'][1][0:46]
+    data_dict[s_global] = [[], []]
+    data_dict[s_global][0] = data_dict[s_1][0][0:46]
+    data_dict[s_global][1] = data_dict[s_1][1][0:46]
 
-    del data_dict['aseg_1']
+    del data_dict[s_1]
 
     # Remove the WM-hypointensities. No value in any subject
     cols_to_remove = ['Left-WM-hypointensities',
@@ -194,9 +205,10 @@ def gen_aparc_special(data_dict, subjectDir):
     for elem in struct_data:
         data_dict[elem[0]][0].append(elem[1])
         try:
-            with open(subjectDir + '/stats/' + elem[2], 'r',
+            with open(op.join(subjectDir, 'stats', elem[2]), 'r',
                       encoding="utf-8") as f:
-                v = [x.split(',')[3].strip() for x in f.readlines() if elem[3] in x]
+                v = [x.split(',')[3].strip() for x in f.readlines()
+                     if elem[3] in x]
                 data_dict[elem[0]][1].append(v[0])
         except Exception:
             data_dict[elem[0]][1].append('NaN')
@@ -205,7 +217,7 @@ def gen_aparc_special(data_dict, subjectDir):
 
 
 def bool_FLAIR(data_dict, subjectDir):
-    if op.isfile(subjectDir + '/mri/FLAIR.mgz'):
+    if op.isfile(op.join(subjectDir, 'mri', 'FLAIR.mgz')):
         data_dict['FLAIR'] = [['Use-T2-FLAIR-for-FreeSurfer'], ['1']]
     else:
         data_dict['FLAIR'] = [['Use-T2-FLAIR-for-FreeSurfer'], ['0']]
@@ -229,7 +241,7 @@ def gen_subsegmentation(data_dict, subjectDir, subject, ctx):
         found = False
         data_dict[struct] = [[], []]
         for fil in struct_data[struct][0]:
-            final_fil = subjectDir + '/FreeSurfer/mri/' + fil
+            final_fil = op.join(subjectDir, 'FreeSurfer', 'mri', fil)
             if op.isfile(final_fil):
                 with open(final_fil, 'r', encoding="utf-8") as f:
                     for lin in f.readlines():
@@ -315,7 +327,6 @@ def remove_first_feature(data_dict, subject):
     return data_dict
 
 def fix_headers(data_dict):
-
     # Applying some general replacing rules for the categories
     replace_rules = [['.', '-'],
                      ['BA_exvivo',        'BA-exvivo'],
@@ -338,20 +349,26 @@ def fix_headers(data_dict):
                 data_dict[new_key] = data_dict.pop(key)
 
     # Renaming some special cases
-    structs = [['aseg_global', 'lhSurfaceHoles', 'aseg_lh_number', 'HolesBeforeFixing'],
-               ['aseg_global', 'rhSurfaceHoles', 'aseg_rh_number', 'HolesBeforeFixing'],
-               ['aseg_global', 'BrainSegVol-to-eTIV', 'aseg_global_volume-ratio', 'BrainSegVol-to-eTIV'],
-               ['aseg_global', 'MaskVol-to-eTIV', 'aseg_global_volume-ratio', 'MaskVol-to-eTIV']]
+    s_global = 'aseg_global'
+    structs = [[s_global, 'lhSurfaceHoles',
+                'aseg_lh_number', 'HolesBeforeFixing'],
+               [s_global, 'rhSurfaceHoles',
+                'aseg_rh_number', 'HolesBeforeFixing'],
+               [s_global, 'BrainSegVol-to-eTIV',
+                'aseg_global_volume-ratio', 'BrainSegVol-to-eTIV'],
+               [s_global, 'MaskVol-to-eTIV',
+                'aseg_global_volume-ratio', 'MaskVol-to-eTIV']]
 
     for struct in structs:
-        index = data_dict[struct[0]][0].index(struct[1])
-        if struct[2] not in data_dict.keys():
-            data_dict[struct[2]] = [struct[3]], [data_dict[struct[0]][1][index]]
-        else:
-            data_dict[struct[2]][0].append(struct[3])
-            data_dict[struct[2]][1].append(data_dict[struct[0]][1][index])
-        del data_dict[struct[0]][0][index]
-        del data_dict[struct[0]][1][index]
+        if struct[1] in data_dict[struct[0]][0]:
+            index = data_dict[struct[0]][0].index(struct[1])
+            if struct[2] not in data_dict.keys():
+                data_dict[struct[2]] = [struct[3]], [data_dict[struct[0]][1][index]]
+            else:
+                data_dict[struct[2]][0].append(struct[3])
+                data_dict[struct[2]][1].append(data_dict[struct[0]][1][index])
+            del data_dict[struct[0]][0][index]
+            del data_dict[struct[0]][1][index]
 
     for metric in ['volume', 'intensity']:
         old_key = 'aseg_' + metric
@@ -382,23 +399,23 @@ def fix_headers(data_dict):
 
         del data_dict[old_key]
 
-    for i in range(len(data_dict['aseg_global'][0])):
-        if data_dict['aseg_global'][0][i].startswith('lh'):
-            new_name = data_dict['aseg_global'][0][i].replace('lh', '').\
+    for i in range(len(data_dict[s_global][0])):
+        if data_dict[s_global][0][i].startswith('lh'):
+            new_name = data_dict[s_global][0][i].replace('lh', '').\
                 replace('Vol', '')
             data_dict['aseg_lh_volume'][0].append(new_name)
-            data_dict['aseg_lh_volume'][1].append(data_dict['aseg_global'][1][i])
-        elif data_dict['aseg_global'][0][i].startswith('rh'):
-            new_name = data_dict['aseg_global'][0][i].replace('rh', '').\
+            data_dict['aseg_lh_volume'][1].append(data_dict[s_global][1][i])
+        elif data_dict[s_global][0][i].startswith('rh'):
+            new_name = data_dict[s_global][0][i].replace('rh', '').\
                 replace('Vol', '')
             data_dict['aseg_rh_volume'][0].append(new_name)
-            data_dict['aseg_rh_volume'][1].append(data_dict['aseg_global'][1][i])
+            data_dict['aseg_rh_volume'][1].append(data_dict[s_global][1][i])
         else:
-            new_name = data_dict['aseg_global'][0][i].replace('Vol', '')
+            new_name = data_dict[s_global][0][i].replace('Vol', '')
             data_dict['aseg_global_volume'][0].append(new_name)
-            data_dict['aseg_global_volume'][1].append(data_dict['aseg_global'][1][i])
+            data_dict['aseg_global_volume'][1].append(data_dict[s_global][1][i])
 
-    del data_dict['aseg_global']
+    del data_dict[s_global]
 
     # Split ThalamNuclei into Left and Right
     data_dict['ThalamNuclei_lh_volume'] = [[], []]
@@ -447,21 +464,21 @@ def fix_headers(data_dict):
     return data_dict
 
 
-def save_data_NaNs(subjects_dir, ctx):
+def save_data_NaNs(subjects_dir, FS_IDPs, ctx):
 
     with open(ctx.get_data('FS/FS_headers.txt'), encoding="utf-8") as f:
         final_headers = [x.replace('\n', '') for x in f.readlines()]
 
     num_NaNs = len(final_headers) - 1
 
-    with open(subjects_dir+'/IDP_files/FS_IDPs.txt', 'w', encoding="utf-8") as f:
+    with open(FS_IDPs, 'w', encoding="utf-8") as f:
         values = ['NaN'] * num_NaNs
         values_str = subjects_dir + " " + " ".join(values)
         f.write(f"{values_str}\n")
         f.close()
 
 
-def save_data(data_dict, subjects_dir, ctx):
+def save_data(data_dict, FS_IDPs, ctx):
 
     with open(ctx.get_data('FS/FS_headers.txt'), encoding="utf-8") as f:
         final_headers = [x.replace('\n', '') for x in f.readlines()]
@@ -479,14 +496,14 @@ def save_data(data_dict, subjects_dir, ctx):
         if x not in temp_headers.keys():
             temp_headers[x] = "NaN"
 
-    with open(subjects_dir+'/IDP_files/FS_IDPs.txt', 'w', encoding="utf-8") as f:
+    with open(FS_IDPs, 'w', encoding="utf-8") as f:
         values = [temp_headers[x] for x in final_headers]
         values_str = " ".join(values)
         f.write(f"{values_str}\n")
         f.close()
 
 
-def save_headers_info(data_dict, subjects_dir, ctx):
+def save_headers_info(data_dict, FS_headers_info, ctx):
 
     with open(ctx.get_data('FS/FS_final_headers.txt'), encoding="utf-8") as f:
         final_headers = [x.replace('\n', '') for x in f.readlines()]
@@ -504,37 +521,37 @@ def save_headers_info(data_dict, subjects_dir, ctx):
         if x not in temp_headers.keys():
             temp_headers[x] = "NaN"
 
-    with open(subjects_dir + '/IDP_files/FS_headers_info.txt', 'w',
-              encoding="utf-8") as f:
+    with open(FS_headers_info, 'w', encoding="utf-8") as f:
         values = [temp_headers[x] for x in final_headers]
         values_str = " ".join(values)
         f.write(f"{values_str}\n")
 
         f.close()
 
-def bb_FS_get_IDPs(ctx):
+def bb_FS_get_IDPs(ctx, env, FreeSurfer_dir, FS_IDPs, FS_headers_info,
+                   FS_stats_dir):
 
-    subject    = ctx.subject
-    subject_ID = 'FreeSurfer'
-    subjectDir = op.join(os.getcwd(), ctx.subject)
-    dataDir    = subjectDir + '/data/'
-    headersDir = subjectDir + '/headers/'
+    subject      = ctx.subject
+    subject_ID   = FreeSurfer_dir.split(op.sep)[-1]
+    subjects_dir = op.join(os.getcwd(), ctx.subject)
+    data_dir     = op.join(os.getcwd(), FreeSurfer_dir, 'data') + op.sep
 
-    if not op.isdir(subjectDir):
+    print(data_dir + " " + subjects_dir + " ")
+    if not op.isdir(subjects_dir):
         raise Exception("Error: FreeSurfer has not been run on this subject")
 
-    check_and_create_dir(dataDir)
-    check_and_create_dir(headersDir)
+    check_and_create_dir(data_dir)
 
-    data_dict = generate_FS_IDP_files(subjectDir, subject_ID, subject, dataDir,
-                                      headersDir, ctx)
-    data_dict = fix_aseg_data(data_dict, subjectDir)
-    data_dict = gen_aparc_special(data_dict, subjectDir)
-    data_dict = gen_subsegmentation(data_dict, subjectDir, subject, ctx)
-    data_dict = bool_FLAIR(data_dict, subjectDir)
+    data_dict = generate_FS_IDP_files(subject_ID, FS_stats_dir, data_dir, ctx,
+                                      env)
+    data_dict = fix_aseg_data(data_dict, subjects_dir)
+    data_dict = gen_aparc_special(data_dict, subjects_dir)
+    data_dict = gen_subsegmentation(data_dict, subjects_dir, subject, ctx)
+    data_dict = bool_FLAIR(data_dict, subjects_dir)
     data_dict = fix_aparc_data(data_dict)
     data_dict = remove_first_feature(data_dict, subject)
     data_dict = fix_headers(data_dict)
 
-    check_consistency(data_dict, subjectDir, ctx)
-    save_data(data_dict, subjectDir, ctx)
+    check_consistency(data_dict, subjects_dir, FS_IDPs, ctx)
+    save_data(data_dict, FS_IDPs, ctx)
+    save_headers_info(data_dict, FS_headers_info, ctx)

bip/pipelines/struct_FS/FS_proc.py

@@ -23,9 +23,10 @@ def run(ctx,
         T1_unbiased:                In,
         T2_FLAIR_unbiased:          In(optional=True),
         logs_dir:                   Ref,
-        FreeSurfer_dir:             Ref,
         fsaverage:                  Ref,
-        rh_entorhinal_exvivo_label: Out):
+        rh_entorhinal_exvivo_label: Out,
+        FreeSurfer_dir:             Out,
+        FS_stats_dir:               Out):
 
     with redirect_logging(job_name(run), outdir=logs_dir):
 

bip/utils/__init__.py

@@ -6,20 +6,16 @@
 
 """The bip.utils package contains a range of miscellaneous utilities. """
 
-
-import            contextlib
-import            logging
+import contextlib
+import logging
 import os.path as op
-import            os
-import            time
-import            errno
-
-import            bip
-
+import os
+import time
+import errno
+import bip
 
 log = logging.getLogger(__name__)
 
-
 @contextlib.contextmanager
 def lockdir(dirname, delay=5):
     """Lock a directory for exclusive access.
@@ -49,11 +45,10 @@ def lockdir(dirname, delay=5):
 
     finally:
         log.debug('Relinquishing lock on %s', dirname)
-        os.close( fd)
+        os.close(fd)
         os.unlink(lockfile)
 
-
-def get_data(filename):
-    """Return the filename, prefixed with the bip/data/ directory path. """
-    filename.replace('/', os.sep)
-    return op.join(bip.BIPDIR, 'data', filename)
+def get_data(file_name):
+    """Return the file_name, prefixed with the bip/data/ directory path. """
+    file_name = file_name.replace('/', os.sep)
+    return op.join(bip.BIPDIR, 'data', file_name)

bip/utils/get_b0s.py

@@ -8,6 +8,8 @@
 #
 # pylint: disable=C0103,E0602,C0114,C0115,C0116,R0913,R0914,R0915
 #
+
+import os.path as op
 import sys
 import argparse
 import os.path
@@ -50,8 +52,10 @@ def main():
                              'If none specified, all will be selected')
     parser.add_argument('-l', dest='B0limit', type=int, default=[100], nargs=1,
                         help='Limit B0 value. (Default 100)')
-    parser.add_argument('-a', dest='bvalFilename', type=str, default='', nargs=1,
-                        help='bval file. (Default: Same basename as the input file)')
+    parser.add_argument('-a', dest='bvalFilename', type=str, default='',
+                        nargs=1,
+                        help='bval file. (Default: Same basename ' +
+                             'as the input file)')
 
     argsa = parser.parse_args()
 
@@ -72,7 +76,7 @@ def main():
     outN    = os.path.basename(outputFile).split('.')[0]
 
     if argsa.bvalFilename == '':
-        bvalFilename = baseDir + "/" + baseN+".bval"
+        bvalFilename = op.join(baseDir, baseN+".bval")
     else:
         bvalFilename = argsa.bvalFilename[0]
 
@@ -97,7 +101,7 @@ def main():
         print("The number of B0 must be positive")
         sys.exit()
 
-    outputIndFile = outDir + '/' + outN + '_indices.txt'
+    outputIndFile = op.join(outDir, outN + '_indices.txt')
 
     get_b0s(inputFile, bvalFilename, outputFile, outputIndFile,
             desiredNumber, B0limit)