Merge pull request #105 from HBClab/enh_3dtcorr

[ENH] seedmap functionality (#105)

Author: jdkent

.circleci/config.yml

@@ -140,6 +140,19 @@ jobs:
             --t1_mask=/data/derivatives/bet/sub-01/anat/sub-01_desc-brainmask_T1w.nii.gz \
             --roiList=/data/derivatives/data/roi_list.txt \
             --compcor_global
+      - run:
+          name: Test seedmapping --compcor_global --motionscrub
+          command: |
+            # run seedmap only
+            docker run -ti --rm=false \
+            -v /tmp/data/ds005:/data \
+            --entrypoint /opt/RestingState/seedVoxelCorrelation.sh \
+            hbclab/restingstate:latest \
+            --epi=/data/derivatives/rsOut/sub-01/nuisanceRegression/compcor_global/nonfiltered_smooth_data_bp_res4d_normandscaled.nii.gz \
+            --motionscrub \
+            --roiList=/data/derivatives/data/roi_list.txt \
+            --compcor_global \
+            --seedmaps
       - run:
           name: Test roi-roi correlations
           command: |
@@ -191,4 +204,4 @@ workflows:
             - get_data
           filters:
             tags:
-              only: /.*/
+              only: /.*/

.circleci/ds005_compcor.txt

@@ -157,15 +157,34 @@
 /sub-01/seedCorrelation/compcor_global/rois/seedQC/UIUC_VIS_rvis_underlay_sagittal.nii
 /sub-01/seedCorrelation/compcor_global/rois/seeds_forQC.txt
 /sub-01/seedCorrelation/compcor_global/rois/seeds_ms.txt
+/sub-01/seedCorrelation/compcor_global/rois/seeds_orig.txt
 /sub-01/seedCorrelation/compcor_global/rois/seeds.txt
 /sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_lvis_mask.nii.gz
+/sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_lvis.png
 /sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_lvis_residvol_ms_ts.txt
 /sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_lvis_residvol_ts.txt
 /sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_lvis_standard.nii.gz
 /sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_rvis_mask.nii.gz
+/sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_rvis.png
 /sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_rvis_residvol_ms_ts.txt
 /sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_rvis_residvol_ts.txt
 /sub-01/seedCorrelation/compcor_global/rois/UIUC_VIS_rvis_standard.nii.gz
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_lvis_corrmap_ms_native.nii
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_lvis_corrmap_ms_native+orig.BRIK
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_lvis_corrmap_ms_native+orig.HEAD
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_lvis_corrmap_ms_standard_masked.nii.gz
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_lvis_corrmap_ms_standard.nii.gz
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_lvis_corrmap_native.nii
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_lvis_corrmap_native+orig.BRIK
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_lvis_corrmap_native+orig.HEAD
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_rvis_corrmap_ms_native.nii
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_rvis_corrmap_ms_native+orig.BRIK
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_rvis_corrmap_ms_native+orig.HEAD
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_rvis_corrmap_ms_standard_masked.nii.gz
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_rvis_corrmap_ms_standard.nii.gz
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_rvis_corrmap_native.nii
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_rvis_corrmap_native+orig.BRIK
+/sub-01/seedCorrelation/compcor_global/seedmaps/UIUC_VIS_rvis_corrmap_native+orig.HEAD
 /sub-01/SigNoise.par
 /sub-01/SigNoisePlot.png
 /sub-01/SNRcalc.txt

.circleci/ds005_compcor_global.txt

@@ -80,6 +80,9 @@ ENV FSLDIR=/usr/share/fsl/5.0 \
     FSLWISH=/usr/bin/wish \
     PATH="/opt/ICA-AROMA:/opt/RestingState:/usr/lib/afni/bin/:/usr/lib/fsl/5.0:$PATH"
 
+# silence gnu parallel
+RUN printf "will cite\n" | parallel --citation
+
 # clean up
 RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*