Merge pull request #27 from mgxd/enh/msm

enh: msm support
bids-apps · May 11, 2018 · 440fa38 · 440fa38
2 parents 20b761f + 04b5000
commit 440fa38
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diff --git a/Dockerfile b/Dockerfile
@@ -27,25 +27,25 @@ RUN apt-get -y update \
     --exclude='freesurfer/average/mult-comp-cor' \
     --exclude='freesurfer/lib/cuda' \
     --exclude='freesurfer/lib/qt' && \
-    apt-get install -y tcsh bc tar libgomp1 perl-modules curl 
+    apt-get install -y tcsh bc tar libgomp1 perl-modules curl
 
 # Set up the environment
-ENV OS Linux
-ENV FS_OVERRIDE 0
-ENV FIX_VERTEX_AREA=
-ENV SUBJECTS_DIR /opt/freesurfer/subjects
-ENV FSF_OUTPUT_FORMAT nii.gz
-ENV MNI_DIR /opt/freesurfer/mni
-ENV LOCAL_DIR /opt/freesurfer/local
-ENV FREESURFER_HOME /opt/freesurfer
-ENV FSFAST_HOME /opt/freesurfer/fsfast
-ENV MINC_BIN_DIR /opt/freesurfer/mni/bin
-ENV MINC_LIB_DIR /opt/freesurfer/mni/lib
-ENV MNI_DATAPATH /opt/freesurfer/mni/data
-ENV FMRI_ANALYSIS_DIR /opt/freesurfer/fsfast
-ENV PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
-ENV MNI_PERL5LIB /opt/freesurfer/mni/lib/perl5/5.8.5
-ENV PATH /opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
+ENV OS=Linux \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA= \
+    SUBJECTS_DIR=/opt/freesurfer/subjects \
+    FSF_OUTPUT_FORMAT=nii.gz \
+    MNI_DIR=/opt/freesurfer/mni \
+    LOCAL_DIR=/opt/freesurfer/local \
+    FREESURFER_HOME=/opt/freesurfer \
+    FSFAST_HOME=/opt/freesurfer/fsfast \
+    MINC_BIN_DIR=/opt/freesurfer/mni/bin \
+    MINC_LIB_DIR=/opt/freesurfer/mni/lib \
+    MNI_DATAPATH=/opt/freesurfer/mni/data \
+    FMRI_ANALYSIS_DIR=/opt/freesurfer/fsfast \
+    PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5 \
+    MNI_PERL5LIB=/opt/freesurfer/mni/lib/perl5/5.8.5 \
+    PATH=/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH
 
 # Install FSL 5.0.9
 RUN apt-get update && \
@@ -57,50 +57,57 @@ RUN apt-get update && \
 
 # Configure environment
 ENV FSLDIR=/usr/share/fsl/5.0
-ENV FSL_DIR="${FSLDIR}"
-ENV FSLOUTPUTTYPE=NIFTI_GZ
-ENV PATH=/usr/lib/fsl/5.0:$PATH
-ENV FSLMULTIFILEQUIT=TRUE
-ENV POSSUMDIR=/usr/share/fsl/5.0
-ENV LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
-ENV FSLTCLSH=/usr/bin/tclsh
-ENV FSLWISH=/usr/bin/wish
-ENV FSLOUTPUTTYPE=NIFTI_GZ
+ENV FSL_DIR="${FSLDIR}" \
+    FSLOUTPUTTYPE=NIFTI_GZ \
+    PATH=/usr/lib/fsl/5.0:$PATH \
+    FSLMULTIFILEQUIT=TRUE \
+    POSSUMDIR=/usr/share/fsl/5.0 \
+    LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH \
+    FSLTCLSH=/usr/bin/tclsh \
+    FSLWISH=/usr/bin/wish \
+    FSLOUTPUTTYPE=NIFTI_GZ
+
 RUN echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh
 
 # Install Connectome Workbench
 RUN apt-get update && apt-get -y install connectome-workbench=1.2.3-1~nd14.04+1
 
 ENV CARET7DIR=/usr/bin
 
-# Install HCP Pipelines
+# Install HCP Pipelines and MSM binaries
+WORKDIR /opt
 RUN apt-get -y update \
     && apt-get install -y --no-install-recommends python-numpy && \
-    wget https://github.com/Washington-University/Pipelines/archive/v3.17.0.tar.gz -O pipelines.tar.gz && \
-    cd /opt/ && \
-    tar zxvf /pipelines.tar.gz && \
+    wget -q https://github.com/Washington-University/Pipelines/archive/v3.17.0.tar.gz -O pipelines.tar.gz && \
+    tar zxf pipelines.tar.gz && \
     mv /opt/Pipelines-* /opt/HCP-Pipelines && \
-    rm /pipelines.tar.gz && \
-    cd / 
+    rm pipelines.tar.gz && \
+    wget -q https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v1/MSM_HOCR_v1-download.tgz -O MSMs.tar.gz && \
+    tar zxf MSMs.tar.gz && \
+    rm MSMs.tar.gz && \
+    mv MSM_HOCR_v1/Ubuntu /opt/HCP-Pipelines/MSMBinaries && \
+    rm -rf MSM_HOCR_v1
+
+WORKDIR /
 
 ENV HCPPIPEDIR=/opt/HCP-Pipelines
-ENV HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
-ENV HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries
-ENV HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config
-ENV HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts
-ENV HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts
-ENV HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts
-ENV HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts
-ENV HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts
-ENV HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts
-ENV HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
-ENV HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts
-ENV HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
-ENV HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
-ENV MSMBin=${HCPPIPEDIR}/MSMBinaries
+ENV HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates \
+    HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries \
+    HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config \
+    HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts \
+    HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts \
+    HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts \
+    HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts \
+    HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts \
+    HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts \
+    HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts \
+    HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts \
+    HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts \
+    HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts \
+    MSMBin=${HCPPIPEDIR}/MSMBinaries
 
-RUN apt-get update && apt-get install -y --no-install-recommends python-pip python-six python-nibabel python-setuptools 
-RUN pip install pybids==0.0.1
+RUN apt-get update && apt-get install -y --no-install-recommends python-pip python-six python-nibabel python-setuptools
+RUN pip install pybids==0.5.1
 ENV PYTHONPATH=""
 
 COPY run.py /run.py

diff --git a/run.py b/run.py
@@ -107,7 +107,7 @@ def run_post_freesurfer(**args):
       '--subcortgraylabels="{HCPPIPEDIR_Config}/FreeSurferSubcorticalLabelTableLut.txt" ' + \
       '--freesurferlabels="{HCPPIPEDIR_Config}/FreeSurferAllLut.txt" ' + \
       '--refmyelinmaps="{HCPPIPEDIR_Templates}/standard_mesh_atlases/Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii" ' + \
-      '--regname="FS" ' + \
+      '--regname="{regname}" ' + \
       '--printcom=""'
     cmd = cmd.format(**args)
     run(cmd, cwd=args["path"], env={"OMP_NUM_THREADS": str(args["n_cpus"])})
@@ -148,7 +148,7 @@ def run_generic_fMRI_surface_processsing(**args):
       '--fmrires={fmrires:s} ' + \
       '--smoothingFWHM={fmrires:s} ' + \
       '--grayordinatesres="{grayordinatesres:s}" ' + \
-      '--regname="FS"'
+      '--regname="{regname}"'
     cmd = cmd.format(**args)
     run(cmd, cwd=args["path"], env={"OMP_NUM_THREADS": str(args["n_cpus"])})
 
@@ -168,7 +168,7 @@ def run_diffusion_processsing(**args):
 
 __version__ = open('/version').read()
 
-parser = argparse.ArgumentParser(description='HCP Pipeliens BIDS App (T1w, T2w, fMRI)')
+parser = argparse.ArgumentParser(description='HCP Pipelines BIDS App (T1w, T2w, fMRI)')
 parser.add_argument('bids_dir', help='The directory with the input dataset '
                     'formatted according to the BIDS standard.')
 parser.add_argument('output_dir', help='The directory where the output files '
@@ -194,6 +194,8 @@ def run_diffusion_processsing(**args):
                    default=['PreFreeSurfer', 'FreeSurfer', 'PostFreeSurfer',
                             'fMRIVolume', 'fMRISurface',
                             'DiffusionPreprocessing'])
+parser.add_argument('--coreg', help='Coregistration method to use',
+                    choices=['MSMSulc', 'FS'], default='MSMSulc')
 parser.add_argument('--license_key', help='FreeSurfer license key - letters and numbers after "*" in the email you received after registration. To register (for free) visit https://surfer.nmr.mgh.harvard.edu/registration.html',
                     required=True)
 parser.add_argument('-v', '--version', action='version',
@@ -205,7 +207,7 @@ def run_diffusion_processsing(**args):
 
 run("bids-validator " + args.bids_dir)
 
-layout = BIDSLayout(args.bids_dir)
+layout = BIDSLayout(args.bids_dir, exclude=['derivatives'])
 subjects_to_analyze = []
 # only for a subset of subjects
 if args.participant_label:
@@ -333,7 +335,8 @@ def run_diffusion_processsing(**args):
                                                  subject="sub-%s"%subject_label,
                                                  grayordinatesres=grayordinatesres,
                                                  lowresmesh=lowresmesh,
-                                                 n_cpus=args.n_cpus))
+                                                 n_cpus=args.n_cpus,
+                                                 regname=args.coreg))
                        ])
         for stage, stage_func in struct_stages_dict.iteritems():
             if stage in args.stages:
@@ -350,12 +353,12 @@ def run_diffusion_processsing(**args):
             if not os.path.exists(fmriscout):
                 fmriscout = "NONE"
 
-            fieldmap_set = layout.get_fieldmap(fmritcs)
-            if fieldmap_set and fieldmap_set["type"] == "epi":
+            fieldmap_set = layout.get_fieldmap(fmritcs, return_list=True)
+            if fieldmap_set and len(fieldmap_set) == 2 and all(item["type"] == "epi" for item in fieldmap_set):
                 SEPhaseNeg = None
                 SEPhasePos = None
-                for fieldmap in fieldmap_set["epi"]:
-                    enc_dir = layout.get_metadata(fieldmap)["PhaseEncodingDirection"]
+                for fieldmap in fieldmap_set:
+                    enc_dir = layout.get_metadata(fieldmap["epi"])["PhaseEncodingDirection"]
                     if "-" in enc_dir:
                         SEPhaseNeg = fieldmap
                     else:
@@ -403,7 +406,8 @@ def run_diffusion_processsing(**args):
                                                        fmrires=fmrires,
                                                        n_cpus=args.n_cpus,
                                                        grayordinatesres=grayordinatesres,
-                                                       lowresmesh=lowresmesh))
+                                                       lowresmesh=lowresmesh,
+                                                       regname=args.coreg))
                                 ])
             for stage, stage_func in func_stages_dict.iteritems():
                 if stage in args.stages: