Various fixes that make pymp2rage Docker work with latest fmriprep/et…

Dockerfile

@@ -28,19 +28,22 @@ RUN bash -c "source activate neuro && pip install lxml --upgrade"
 RUN apt-get update -qq && apt-get install -y python python-pip python-dev build-essential software-properties-common openjdk-8-jdk
 RUN ln -svT "/usr/lib/jvm/java-8-openjdk-$(dpkg --print-architecture)" /docker-java-home
 ENV JAVA_HOME /docker-java-home
-ENV JCC_JDK /docker-java-home
+ENV JCC_JDK /docker-java-home 
 RUN apt-get install -y jcc
 
-COPY nighres /nighres
+COPY nighres /nighres 
 
 RUN cd /nighres \
-    && python3 -m pip install --upgrade pip jcc \
-    && ./build.sh \
+    && bash -c "source activate neuro && pip install jcc" \
+    && bash -c "./build_conda.sh neuro" \
     && bash -c "source activate neuro && python setup.py develop"
 
 COPY ./analysis /src
 COPY nipype.cfg /root/.nipype/nipype.cfg
 
+RUN bash -c "source activate neuro && pip uninstall -y pandas && pip install pandas==0.23" \
+    && bash -c "source activate neuro && pip uninstall -y templateflow && pip install templateflow"
+
 COPY ./fmriprep /fmriprep
 RUN bash -c "source activate neuro && pip uninstall -y fmriprep && cd /fmriprep && python setup.py develop"
 
@@ -53,3 +56,5 @@ RUN bash -c "source activate neuro && pip uninstall -y pybids && cd /pybids && p
 COPY spynoza /spynoza
 RUN bash -c "source activate neuro && pip uninstall -y spynoza && cd /pybids && python setup.py develop"
 
+RUN bash -c "source activate neuro && pip install scikit-image --upgrade"
+RUN bash -c "source activate neuro && pip install templateflow --upgrade"

analysis/combine_scans.py

@@ -1,6 +1,6 @@
 import argparse
-from fmriprep.interfaces import DerivativesDataSink
 from bids import BIDSLayout
+from fmriprep.interfaces import DerivativesDataSink
 import re
 import pandas as pd
 import os

analysis/mask_mp2rage.py

@@ -112,7 +112,7 @@ def main(sourcedata,
     if session is None:
         session = '.*'
 
-    derivatives_layout = BIDSLayout(os.path.join(derivatives, 'averaged_mp2rages'))
+    derivatives_layout = BIDSLayout(os.path.join(derivatives, 'averaged_mp2rages'), validate=False)
 
     inv2 = get_bids_file(derivatives_layout, 
                          subject,
@@ -232,8 +232,7 @@ def init_masking_wf(name='mask_wf',
                                          keep_dtype=False,
                                          out_path_base='masked_mp2rages',
                                          suffix='T1map',
-                                         desc='masked',
-                                         space='average'),
+                                         desc='masked'),
                                          name='ds_t1map')
 
     wf.connect(inputnode, 't1map', ds_t1map, 'source_file')

analysis/utils.py

@@ -15,6 +15,7 @@ def get_inv(mp2rage_parameters, inv=1, echo=1):
 def fit_mp2rage(mp2rage_parameters, return_images=['t1w_uni', 't1map']):
     import pymp2rage
     import os
+    print(mp2rage_parameters)
 
     if 'echo_times' in mp2rage_parameters:
         mp2rage = pymp2rage.MEMP2RAGE(**mp2rage_parameters)
@@ -33,29 +34,33 @@ def get_mp2rage_pars(sourcedata, subject, session, acquisition):
     from bids import BIDSLayout
     import re
     import os
+    import os.path as op
     import glob
     import json
     import numpy as np
 
-    layout = BIDSLayout(sourcedata)
+    layout = BIDSLayout(sourcedata, 
+		    validate=False)
 
     mp2rage_files = layout.get(subject=subject, 
                                session=session, 
                                acquisition=acquisition,
                                suffix='MPRAGE', 
                                extensions=['.nii', '.nii.gz'])
+
     print(mp2rage_files)
 
     reg = re.compile('.*/sub-(?P<subject>.+)_ses-(?P<session>.+)_acq-(?P<acquisition>.+)_inv-(?P<inv>[0-9]+)(_echo-(?P<echo>[0-9]+))?(_part-(?P<part>.+))?_MPRAGE.(?P<extension>nii|nii\.gz|json)')
 
     data = []
     for file in mp2rage_files:
-        print(file.filename)
-        if not reg.match(file.filename):
-            print('ERROR WITH {}'.format(file))
-        data.append(reg.match(file.filename).groupdict())
-        data[-1]['filename'] = file.filename
+        print(file.path)
+        if not reg.match(file.path):
+            print('ERROR WITH {}'.format(file.path))
+        data.append(reg.match(file.path).groupdict())
+        data[-1]['filename'] = file.path
     data = pd.DataFrame(data)
+    print(data)
 
     folder = os.path.dirname(data.iloc[0].filename)
     json_files = glob.glob(os.path.join(folder, '*.json'))
@@ -68,7 +73,9 @@ def get_mp2rage_pars(sourcedata, subject, session, acquisition):
                 json_data[-1].update(json.load(f))
 
     json_data = pd.DataFrame(json_data)
-    json_data.drop(columns=['part', 'extension'], inplace=True)
+    print(json_data)
+    json_data.drop('part', axis=1, inplace=True)
+    json_data.drop('extension', axis=1, inplace=True)
     data = data.merge(json_data, on=['subject', 'session', 'acquisition', 'inv', 'echo'])
 
     data.drop(columns=['subject', 'session'])
@@ -82,7 +89,7 @@ def get_mp2rage_pars(sourcedata, subject, session, acquisition):
     B1map = layout.get(subject=subject, session=session, suffix='B1map', extensions=['.nii', '.nii.gz'])
 
     if len(B1map) > 0:
-        B1map = B1map[0].filename
+        B1map = B1map[0].path
         data['B1map'] = B1map
 
     multi_echo_bool = len(data.loc[acquisition,2, :, 'mag']) > 2

go

@@ -1 +1,5 @@
+export FREESURFER_HOME=/home/freesurfer/license.txt
+export DERIVATIVES=/home/shared/2018/visual/SB-prep/SB-ref/derivatives/mp2rage_preproc_out
+export SOURCEDATA=/home/shared/2018/visual/SB-prep/SB-ref/sourcedata
 docker-compose run --rm mp2rage_preproc
+