wip/enh/brk: updated dockerfile. added a cli for data. updated the workflow to save outlier indices in report. updated viewer to show outliers on line chart. brk: updated viewer to have brainsprites, but they are kind of broken right now

Author: akeshavan

Dockerfile-dmriprep

@@ -2,4 +2,5 @@ FROM dmriprep:dev
 
 ADD . /dmriprep
 WORKDIR /dmriprep
-RUN /neurodocker/startup.sh python /dmriprep/setup.py install
+RUN /neurodocker/startup.sh python setup.py install
+WORKDIR /

dmriprep/cli.py

@@ -5,6 +5,7 @@
 import click
 from . import run
 from . import io
+from .data import get_dataset
 import os
 
 
@@ -50,6 +51,13 @@ def main(participant_label, bids_dir, output_dir, analysis_level="participant"):
 
     return 0
 
+@click.command()
+@click.argument('output_dir',
+                )
+def data(output_dir):
+    get_dataset(os.path.abspath(output_dir))
+    print('done')
+
 
 if __name__ == "__main__":
     sys.exit(main())  # pragma: no cover

dmriprep/qc.py

@@ -212,6 +212,7 @@ def createB0_ColorFA_Mask_Sprites(b0_file, colorFA_file, mask_file):
 
 def create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
                        color_fa_file, anat_mask_file,
+                       outlier_indices,
                        outpath=op.abspath('./report.json')):
 
     report = {}
@@ -223,6 +224,7 @@ def create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
     report['b0'] = b0
     report['colorFA'] = colorFA
     report['anat_mask'] = mask
+    report['outlier_volumes'] = outlier_indices.tolist()
 
     with open(eddy_report, 'r') as f:
         report['eddy_report'] = f.readlines()

dmriprep/run.py

@@ -379,6 +379,7 @@ def drop_outliers_fn(in_file, in_bval, in_bvec, drop_scans):
         import nibabel as nib
         import numpy as np
         import os.path as op
+        from nipype.utils.filemanip import fname_presuffix
 
         img = nib.load(op.abspath(in_file))
         img_data = img.get_fdata()
@@ -387,17 +388,17 @@ def drop_outliers_fn(in_file, in_bval, in_bvec, drop_scans):
 
         root, ext1 = op.splitext(in_file)
         root, ext0 = op.splitext(root)
-        out_file = ''.join([root + "_thinned", ext0, ext1])
+        out_file = fname_presuffix(in_file, suffix="_thinned", newpath=op.abspath('.')) #''.join([root + "_thinned", ext0, ext1])
         nib.save(img_thinned, op.abspath(out_file))
 
         bval = np.loadtxt(in_bval)
         bval_thinned = np.delete(bval, drop_scans, axis=0)
-        out_bval = '_thinned'.join(op.splitext(in_bval))
+        out_bval = fname_presuffix(in_bval, suffix="_thinned", newpath=op.abspath('.'))
         np.savetxt(out_bval, bval_thinned)
 
         bvec = np.loadtxt(in_bvec)
         bvec_thinned = np.delete(bvec, drop_scans, axis=1)
-        out_bvec = '_thinned'.join(op.splitext(in_bvec))
+        out_bvec = fname_presuffix(in_bvec, suffix="_thinned", newpath=op.abspath('.'))
         np.savetxt(out_bvec, bvec_thinned)
 
         return out_file, out_bval, out_bvec
@@ -546,24 +547,25 @@ def get_orig(subjects_dir, sub):
     wf.connect(convert1, "out_file", datasink, "dmriprep.anat.@anat")
 
     def reportNodeFunc(dwi_corrected_file, eddy_rms, eddy_report,
-                       color_fa_file, anat_mask_file):
+                       color_fa_file, anat_mask_file, outlier_indices):
         from dmriprep.qc import create_report_json
 
         report = create_report_json(dwi_corrected_file, eddy_rms, eddy_report,
-                                    color_fa_file, anat_mask_file)
+                                    color_fa_file, anat_mask_file, outlier_indices)
         return report
 
     reportNode = pe.Node(niu.Function(
         input_names=['dwi_corrected_file', 'eddy_rms',
                      'eddy_report', 'color_fa_file',
-                     'anat_mask_file'],
+                     'anat_mask_file', 'outlier_indices'],
         output_names=['report'],
         function=reportNodeFunc
     ), name="reportJSON")
 
     wf.connect(prep, "outputnode.out_file", reportNode, 'dwi_corrected_file')
     wf.connect(prep, "fsl_eddy.out_movement_rms", reportNode, 'eddy_rms')
     wf.connect(prep, "fsl_eddy.out_outlier_report", reportNode, 'eddy_report')
+    wf.connect(id_outliers_node, 'drop_scans', reportNode, 'outlier_indices')
     wf.connect(threshold2, "binary_file", reportNode, 'anat_mask_file')
     wf.connect(get_tensor, "color_fa_file", reportNode, 'color_fa_file')
 
@@ -574,5 +576,5 @@ def reportNodeFunc(dwi_corrected_file, eddy_rms, eddy_report,
     wf.run()
 
     copyfile(bval_file, op.join(
-        out_dir, "dmriprep", "dwi", op.split(bval_file)[1]
+        op.abspath(out_dir), "dmriprep", "dwi", op.split(bval_file)[1]
     ))

dmriprepViewer/package-lock.json

@@ -16,6 +16,7 @@
   "dependencies": {
     "axios": "^0.18.0",
     "bootstrap-vue": "^2.0.0-rc.11",
+    "brainsprite.js": "git+https://[email protected]/SIMEXP/brainsprite.js.git",
     "d3": "^5.7.0",
     "vue": "^2.5.2",
     "vue-router": "^3.0.1",

dmriprepViewer/package.json

@@ -7,6 +7,7 @@
 <script>
 import Vue from 'vue';
 import BootstrapVue from 'bootstrap-vue';
+// eslint-disable-next-line
 import 'bootstrap/dist/css/bootstrap.css';
 import 'bootstrap-vue/dist/bootstrap-vue.css';
 

dmriprepViewer/src/App.vue

@@ -17,7 +17,7 @@
         </b-input-group-append>
       </b-input-group>
 
-      <report v-if="report.b0" :report="report"></report>
+      <report v-if="report.b0" :reportProp="report"></report>
   </b-container>
 </template>
 
@@ -27,6 +27,7 @@ import sprite4d from './Sprite4D';
 import lineChart from './LineChart';
 import report from './Report';
 
+
 export default {
   name: 'HelloWorld',
   components: {

dmriprepViewer/src/components/HelloWorld.vue

@@ -153,6 +153,17 @@ export default {
         .attr('stroke-width', 1.5)
         .attr('d', line2);
 
+      this.g.selectAll('.outlier')
+        .data(this.outlier_indices)
+        .enter()
+        .append('rect')
+        .attr('class', 'outlier')
+        .attr('x', i => self.x(i) - 1.5)
+        .attr('y', () => self.y(maxY))
+        .attr('width', '3px')
+        .attr('height', () => `${self.height}px`)
+        .attr('fill', 'black');
+
 
       this.svg.on('mousemove', () => {
         // const x0 = self.x.invert(d3.mouse(this)[0]);
@@ -168,7 +179,7 @@ export default {
     this.initAx();
     this.plotData();
   },
-  props: ['ylabel', 'xlabel', 'data', 'id', 'highlightIdx'],
+  props: ['ylabel', 'xlabel', 'data', 'id', 'highlightIdx', 'outlier_indices'],
 };
 </script>
 

dmriprepViewer/src/components/LineChart.vue

@@ -34,6 +34,7 @@
         <div style="height: 200px; width: 100%; display: inline-flex;">
           <line-chart id="motion_params"
            :data="report.eddy_params"
+           :outlier_indices="report.outlier_volumes"
            xlabel="TR"
            ylabel="RMS"
            :highlightIdx="time"
@@ -44,59 +45,31 @@
       <h2 class="mt-3 pt-3">Registration + Brain Mask</h2>
       <p class="lead">Brain mask computed on T1w, and mapped to B0</p>
 
-      <sprite4d
-        :key="'bmask'+2"
-        :M="report.b0.M"
-        :N="report.b0.N"
-        :num_slices="report.b0.num_slices"
-        id="b0_mask"
-        :pix="report.b0.pix"
-        :time="spriteSlice"
-        :img="report.b0.img"
-        opacity="1"
-      ></sprite4d>
-      <sprite4d
-        :key="'anat_mask'+1"
-        :M="report.anat_mask.M"
-        :N="report.anat_mask.N"
-        :num_slices="report.anat_mask.num_slices"
-        id="anat_mask"
-        :pix="report.anat_mask.pix"
-        :time="spriteSlice"
-        :img="report.anat_mask.img"
-        :overlayMode="true"
-        opacity="1"
-      ></sprite4d>
-      <vue-slider ref="timeSlider"
-       v-model="spriteSlice" :min="0"
-       :max="report.b0.num_slices-1"></vue-slider>
+      <BrainSprite
+        id="brainMaskSprite"
+        ref="brainMaskSprite"
+        :base_dim_x="report.b0.pix"
+        :base_dim_y="report.b0.pix"
+        :overlay_dim_x="report.anat_mask.pix"
+        :overlay_dim_y="report.anat_mask.pix"
+        :base="report.b0.img"
+        :overlay="report.anat_mask.img"
+      />
 
       <h2 class="mt-3 pt-3">DTI: ColorFA</h2>
       <p class="lead">Color FA mapped on B0</p>
 
-      <sprite4d
-        key="bmask1"
-        :M="report.b0.M"
-        :N="report.b0.N"
-        :num_slices="report.b0.num_slices"
-        id="b0_mask"
-        :pix="report.b0.pix"
-        :time="spriteSlice"
-        :img="report.b0.img"
-        opacity="1"
-      ></sprite4d>
-      <sprite4d
-        key="colorfa_mask"
-        :M="report.colorFA.M"
-        :N="report.colorFA.N"
-        :num_slices="report.colorFA.num_slices"
-        id="colorfa_mask"
-        :pix="report.colorFA.pix"
-        :time="spriteSlice"
-        :img="report.colorFA.img"
-        :overlayMode="true"
-        opacity="0.5"
-      ></sprite4d>
+      <BrainSprite
+        id="colorFASprite"
+        ref="colorFASprite"
+        :base_dim_x="report.b0.pix"
+        :base_dim_y="report.b0.pix"
+        :overlay_dim_x="report.colorFA.pix"
+        :overlay_dim_y="report.colorFA.pix"
+        :base="report.b0.img"
+        :overlay="report.colorFA.img"
+      />
+
     </div>
   </div>
 </template>
@@ -106,18 +79,21 @@ import axios from 'axios';
 import vueSlider from 'vue-slider-component';
 import sprite4d from './Sprite4D';
 import lineChart from './LineChart';
+import BrainSprite from './BrainSprite.vue';
 
 export default {
   name: 'report',
   components: {
     sprite4d,
     vueSlider,
     lineChart,
+    BrainSprite,
   },
   data() {
     return {
       time: 0,
       spriteSlice: 0,
+      report: null,
     };
   },
   methods: {
@@ -139,11 +115,23 @@ export default {
     }
   },
   mounted() {
-    if (this.report) {
-      this.spriteSlice = this.get_mid_slice();
+    if (this.reportProp) {
+      this.report = this.reportProp;
     }
+    this.$nextTick(() => {
+      if (this.report) {
+        this.spriteSlice = this.get_mid_slice();
+        // this.$refs.brainMaskSprite.initBrainSprite();
+        // this.$refs.colorFASprite.initBrainSprite();
+      }
+    });
   },
   watch: {
+    reportProp() {
+      if (this.reportProp) {
+        this.report = this.reportProp;
+      }
+    },
     report() {
       if (this.report) {
         this.spriteSlice = this.get_mid_slice();
@@ -163,7 +151,7 @@ export default {
     },
   },
   props: {
-    report: Object,
+    reportProp: Object,
   },
 };
 </script>