[RTM] Add ICA component plots to MRIQC

CHANGES.txt

@@ -1,6 +1,7 @@
 Release x.x.x
 =============
 
+* [ENH] Optional ICA reports for identifying spatiotemporal artifacts (#412)
 * [ENH] Add --profile flag (#435)
 * [ENH] Crashfiles are saved in plain text to improve portability (#434)
 

circle.yml

@@ -30,7 +30,7 @@ test:
     # Test mriqcp
     - docker run -i -v /etc/localtime:/etc/localtime:ro -v ${CIRCLE_TEST_REPORTS}:/scratch -w /opt/src/mriqc --entrypoint="/usr/bin/run_tests" poldracklab/mriqc:latest :
         timeout: 2600
-    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/data:/data:ro -v $SCRATCH:/scratch -w /scratch poldracklab/mriqc:latest /data/${TEST_DATA_NAME} out/ participant --testing --verbose-reports --profile :
+    - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/data:/data:ro -v $SCRATCH:/scratch -w /scratch poldracklab/mriqc:latest /data/${TEST_DATA_NAME} out/ participant --testing --verbose-reports --profile --n_proc 2 --ants-nthreads 1 --ica :
         timeout: 3200
     - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/data:/data:ro -v $SCRATCH:/scratch -w /scratch poldracklab/mriqc:latest /data/${TEST_DATA_NAME} out/ group -m bold
     - docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/data:/data:ro -v $SCRATCH:/scratch -w /scratch poldracklab/mriqc:latest /data/${TEST_DATA_NAME} out/ group -m T1w

docker/Dockerfile_py27

@@ -46,6 +46,16 @@ RUN conda config --add channels conda-forge && \
     conda install -y numpy>=1.12.0 scipy matplotlib && \
     python -c "from matplotlib import font_manager"
 
+# Installing WEBP tools
+RUN curl -sSLO "http://downloads.webmproject.org/releases/webp/libwebp-0.5.2-linux-x86-64.tar.gz" && \
+  tar -xf libwebp-0.5.2-linux-x86-64.tar.gz && cd libwebp-0.5.2-linux-x86-64/bin && \
+  mv cwebp /usr/local/bin/ && rm -rf libwebp-0.5.2-linux-x86-64
+
+# Installing SVGO
+RUN curl -sL https://deb.nodesource.com/setup_7.x | bash -
+RUN apt-get install -y nodejs
+RUN npm install -g svgo
+
 # Install mriqc
 WORKDIR /opt/src/mriqc
 COPY . /opt/src/mriqc/

docker/Dockerfile_py35

@@ -48,6 +48,16 @@ RUN conda config --add channels conda-forge && \
     conda install -y numpy>=1.12.0 scipy matplotlib && \
     python -c "from matplotlib import font_manager"
 
+# Installing WEBP tools
+RUN curl -sSLO "http://downloads.webmproject.org/releases/webp/libwebp-0.5.2-linux-x86-64.tar.gz" && \
+  tar -xf libwebp-0.5.2-linux-x86-64.tar.gz && cd libwebp-0.5.2-linux-x86-64/bin && \
+  mv cwebp /usr/local/bin/ && rm -rf libwebp-0.5.2-linux-x86-64
+
+# Installing SVGO
+RUN curl -sL https://deb.nodesource.com/setup_7.x | bash -
+RUN apt-get install -y nodejs
+RUN npm install -g svgo
+
 COPY . /opt/src/mriqc/
 
 RUN pip install -r /opt/src/mriqc/requirements.txt

mriqc/bin/mriqc_run.py

@@ -76,6 +76,9 @@ def main():
                          help='Do not run the workflow.')
     g_input.add_argument('--use-plugin', action='store', default=None,
                          help='nipype plugin configuration file')
+    g_input.add_argument('--ica', action='store_true', default=False,
+                         help='Run ICA on the raw data and include the components'
+                              'in the individual reports (slow but potentially very insightful)')
 
     g_input.add_argument('--testing', action='store_true', default=False,
                          help='use testing settings for a minimal footprint')
@@ -136,26 +139,6 @@ def main():
     if opts.n_procs is not None:
         n_procs = opts.n_procs
 
-    # Check physical memory
-    total_memory = opts.mem_gb
-    if total_memory < 0:
-        try:
-            from psutil import virtual_memory
-            total_memory = virtual_memory().total // (1024 ** 3) + 1
-        except ImportError:
-            MRIQC_LOG.warn('Total physical memory could not be estimated, using %d'
-                           'GB as default', DEFAULT_MEM_GB)
-            total_memory = DEFAULT_MEM_GB
-
-    if total_memory > 0:
-        av_procs = total_memory // 4
-        if av_procs < 1:
-            MRIQC_LOG.warn('Total physical memory is less than 4GB, memory allocation'
-                           ' problems are likely to occur.')
-            n_procs = 1
-        elif n_procs > av_procs:
-            n_procs = av_procs
-
     settings = {
         'bids_dir': bids_dir,
         'write_graph': opts.write_graph,
@@ -168,7 +151,8 @@ def main():
         'output_dir': op.abspath(opts.output_dir),
         'work_dir': op.abspath(opts.work_dir),
         'verbose_reports': opts.verbose_reports or opts.testing,
-        'float32': opts.float32
+        'float32': opts.float32,
+        'ica': opts.ica
     }
 
     if opts.hmc_afni:
@@ -226,8 +210,8 @@ def main():
         if settings['n_procs'] > 1:
             plugin_settings['plugin'] = 'MultiProc'
             plugin_settings['plugin_args'] = {'n_procs': settings['n_procs']}
-            if total_memory > 0:
-                plugin_settings['plugin_args']['memory_gb'] = total_memory
+            if opts.mem_gb:
+                plugin_settings['plugin_args']['memory_gb'] = opts.mem_gb
 
     MRIQC_LOG.info(
         'Running MRIQC-%s (analysis_levels=[%s], participant_label=%s)\n\tSettings=%s',

mriqc/data/reports/group.html

@@ -63,29 +63,41 @@ <h2>Summary</h2>
             }
 
         });
+        if (data.length > 0) {
+            chart1 = makeDistroChart({
+                data: data,
+                xName: 'iqm',
+                yName: 'value',
+                selector: "#chart-group" + group,
+                chartSize: {height: 300, width: 100 + 60 * nIQMs},
+                constrainExtremes: false,
+                modality: '{{ modality }}'
+            });
+            chart1.renderDataPlots();
+            chart1.dataPlots.change({
+                showPlot: true,
+                plotType: 20,
+                padding: 20,
+                showBeanLines: false
+            });
+            chart1.renderBoxPlot();
+            chart1.boxPlots.show({
+                showWhiskers: true,
+                showOutliers: false,
+                boxWidth: 15,
+                lineWidth: 15,
+                padding: -10,
+                colors: ['#555']
+            });
 
-        chart1 = makeDistroChart({
-            data:data,
-            xName:'iqm',
-            yName:'value',
-            selector:"#chart-group" + group,
-            chartSize:{height:300, width:100 + 60 * nIQMs},
-            constrainExtremes:false,
-            modality: '{{ modality }}'
-        });
-        chart1.renderDataPlots();
-        chart1.dataPlots.change({showPlot:true, plotType:20, padding: 20, showBeanLines:false});
-        chart1.renderBoxPlot();
-        chart1.boxPlots.show({showWhiskers:true,showOutliers:false,boxWidth:15,lineWidth:15,
-            padding: -10, colors:['#555']});
-
-        // chart1.renderNotchBoxes({showNotchBox:false});
-        // chart1.renderViolinPlot({showViolinPlot:false});
-        // chart1.violinPlots.show({reset:true,clamp:0});
-        // chart1.dataPlots.show({showPlot:false,showBeanLines:true, colors:['#555']})
+            // chart1.renderNotchBoxes({showNotchBox:false});
+            // chart1.renderViolinPlot({showViolinPlot:false});
+            // chart1.violinPlots.show({reset:true,clamp:0});
+            // chart1.dataPlots.show({showPlot:false,showBeanLines:true, colors:['#555']})
 
-        //chart1.notchBoxes.hide();
-        //chart1.boxPlots.hide();
+            //chart1.notchBoxes.hide();
+            //chart1.boxPlots.hide();
+        }
     }
 
     {% for data_csv in csv_groups %}

mriqc/workflows/anatomical.py

@@ -97,6 +97,8 @@ def anat_qc_workflow(dataset, settings, mod='T1w', name='anatMRIQC'):
     norm = pe.Node(RobustMNINormalization(
         num_threads=settings.get('ants_nthreads', 6), template='mni_icbm152_nlin_asym_09c',
         testing=settings.get('testing', False), generate_report=True), name='SpatialNormalization')
+    norm.interface.num_threads = settings.get('ants_nthreads', 6)
+
     if mod == 'T1w':
         norm.inputs.reference = 'T1'
     elif mod == 'T2w':

mriqc/workflows/core.py

@@ -10,11 +10,14 @@
 from __future__ import print_function, division, absolute_import, unicode_literals
 from mriqc.workflows.anatomical import anat_qc_workflow
 from mriqc.workflows.functional import fmri_qc_workflow
+import os
 
 
 def build_workflow(dataset, mod, settings=None):
     """ Multi-subject anatomical workflow wrapper """
 
+    settings["biggest_file_size_gb"] = _get_biggest_file_size_gb(dataset)
+
     if mod == 'bold':
         workflow = fmri_qc_workflow(dataset, settings=settings)
     elif mod == 'T1w':
@@ -28,3 +31,11 @@ def build_workflow(dataset, mod, settings=None):
     if settings.get('write_graph', False):
         workflow.write_graph()
     return workflow
+
+def _get_biggest_file_size_gb(files):
+    max_size = 0
+    for file in files:
+        size = os.path.getsize(file)/(1024*1024*1024)
+        if size > max_size:
+            max_size = size
+    return max_size