Merge pull request #280 from Shotgunosine/fix_afni_tsnr

FIX: AFNI TSNR calculation, ADD: BlurToFWHM,  ADD: testing outputs against reference

.circleci/config.yml

@@ -67,30 +67,26 @@ jobs:
           path: /tmp/src
       - restore_cache:
           keys:
-            - ds003-v0-{{ .Branch }}-
-            - ds003-v0-master-
-            - ds003-v0-
+            - ds003-v1-{{ .Branch }}-
+            - ds003-v1-master-
+            - ds003-v1-
       - run:
           name: Set git ID
           command: |
             git config --global user.name 'FitLins CircleCI User'
             git config --global user.email 'crn.poldracklab@gmail.com'
       - run:
-          name: Install fMRIPrep derivatives of ds000003
+          name: Install fMRIPrep derivatives of ds000003 and reference data
           command: |
-            datalad install -r ///labs/poldrack/ds003_fmriprep
-            datalad update ds003_fmriprep/
-            datalad get ds003_fmriprep/sub-0{1,2,3}/func/*_space-MNI152NLin2009cAsym_desc-*.nii.gz \
-                        ds003_fmriprep/sub-0{1,2,3}/func/*_desc-confounds_*.tsv \
-                        ds003_fmriprep/dataset_description.json \
-                        ds003_fmriprep/sub-*/*/*.json
-      - run:
-          name: Download a model for ds000003
-          command: |
-              mkdir -p ds003_models
-              cp /tmp/src/examples/models/ds000003/models/model-001_smdl.json ds003_models/
+            datalad install -r -s https://gin.g-node.org/shotgunosine/fitlins_tests
+            datalad update --merge fitlins_tests
+            datalad get fitlins_tests/ds003/ds003_fmriprep/sub-0{1,2,3}/func/*_space-MNI152NLin2009cAsym_desc-*.nii.gz \
+                                    fitlins_tests/ds003/ds003_fmriprep/sub-0{1,2,3}/func/*_desc-confounds_*.tsv \
+                                    fitlins_tests/ds003/ds003_fmriprep/dataset_description.json \
+                                    fitlins_tests/ds003/ds003_fmriprep/sub-*/*/*.json
+            datalad get -r fitlins_tests/ds003/nistats_smooth/ fitlins_tests/ds003/afni_smooth/ fitlins_tests/ds003/afni_blurto/ fitlins_tests/ds003/nistats_blurto/
       - save_cache:
-         key: ds003-v0-{{ .Branch }}-{{ .BuildNum }}
+         key: ds003-v1-{{ .Branch }}-{{ .BuildNum }}
          paths:
             - /tmp/data
 
@@ -153,7 +149,9 @@ jobs:
                 -e COVERAGE_FILE=/scratch/.coverage.pytest \
                 --entrypoint="/neurodocker/startup.sh" \
                 poldracklab/fitlins:latest \
-                pytest --cov=fitlins --cov-report xml:/scratch/cov_pytest.xml /src/fitlins
+                pytest --cov=fitlins --cov-report xml:/scratch/cov_pytest.xml \
+                 --cov-config /src/fitlins/docker/multiproc.coveragerc \
+                 --ignore-glob=/src/fitlins/fitlins/tests/* /src/fitlins
       - run:
           name: Submit pytest coverage
           command: |
@@ -164,7 +162,7 @@ jobs:
 
   test_ds003:
     parameters:
-      estimator:
+      test_name:
         type: string
     machine:
       image: circleci/classic:201711-01
@@ -177,9 +175,9 @@ jobs:
             - docker-v0-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
-            - ds003-v0-{{ .Branch }}-
-            - ds003-v0-master-
-            - ds003-v0-
+            - ds003-v1-{{ .Branch }}-
+            - ds003-v1-master-
+            - ds003-v1-
       - run:
           name: Load Docker image layer cache
           no_output_timeout: 30m
@@ -193,40 +191,36 @@ jobs:
             fi
       - run:
           name: Run FitLins
-          no_output_timeout: 2h
+          no_output_timeout: 4h
           command: |
             mkdir -p /tmp/ds003/work /tmp/ds003/derivatives
             chmod 777 /tmp/ds003/work /tmp/ds003/derivatives
             export CONDA_PREFIX=/opt/miniconda-latest/envs/neuro
-            docker run --rm -v /tmp/data/ds003_fmriprep:/data:ro \
+            docker run --rm -v /tmp/data/fitlins_tests:/data:ro \
                 -v /tmp/ds003/derivatives:/out \
                 -v /tmp/ds003/work:/scratch \
-                -v /tmp/data/ds003_models:/models \
-                -e COVERAGE_FILE=/scratch/.coverage \
+                -e COVERAGE_FILE=/scratch/.coverage_<< parameters.test_name >> \
                 --entrypoint="/neurodocker/startup.sh" \
                 poldracklab/fitlins:latest \
-                coverage run \
-                --rcfile /src/fitlins/docker/multiproc.coveragerc \
-                $CONDA_PREFIX/bin/fitlins /data/sourcedata /out dataset \
-                -d /data -m /models/model-001_smdl.json -w /scratch \
-                --participant-label 01 02 03 --space MNI152NLin2009cAsym \
-                --estimator << parameters.estimator >> \
-                --n-cpus 2 --mem-gb 4 -vv
+                pytest --cov=fitlins \
+                --cov-config /src/fitlins/docker/multiproc.coveragerc \
+                --cov-report xml:/scratch/.coverage_pytest_<< parameters.test_name >>.xml \
+                $CONDA_PREFIX/lib/python3.6/site-packages/fitlins/tests \
+                --fitlins-path=$CONDA_PREFIX/bin/fitlins \
+                --bids-dir=/data/ds003/ds003_fmriprep/sourcedata \
+                --output-dir=/out \
+                --derivatives=/data/ds003/ds003_fmriprep \
+                --model=/data/ds003/models/model-001_smdl.json \
+                --work-dir=/scratch \
+                --test-name=<< parameters.test_name >> \
+                --database-path=/out/ds003_database \
+                --reference-dir=/data/ds003
       - run:
           name: Combine coverage and submit
           command: |
-              # combine coverage
-              docker run --rm \
-                -v /tmp/ds003/work:/scratch \
-                -w /scratch \
-                --entrypoint="/neurodocker/startup.sh" \
-                poldracklab/fitlins:latest \
-                bash -c "coverage combine /scratch/.coverage* \
-                         && coverage xml"
-              # submit coverage
               bash <(curl --retry 5 -s https://codecov.io/bash) \
-                -f /tmp/ds003/work/coverage.xml \
-                -F << parameters.estimator >> \
+                -f /tmp/ds003/work/.coverage_pytest_<< parameters.test_name >>.xml \
+                -F << parameters.test_name >> \
                 -e CIRCLE_JOB
       - store_artifacts:
           path: /tmp/ds003
@@ -243,9 +237,9 @@ jobs:
             - docker-v0-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
-            - ds003-v0-{{ .Branch }}-
-            - ds003-v0-master-
-            - ds003-v0-
+            - ds003-v1-{{ .Branch }}-
+            - ds003-v1-master-
+            - ds003-v1-
       - run:
           name: Load Docker image layer cache
           no_output_timeout: 30m
@@ -264,10 +258,10 @@ jobs:
             mkdir -p /tmp/ds003/work /tmp/ds003/derivatives
             chmod 777 /tmp/ds003/work /tmp/ds003/derivatives
             export CONDA_PREFIX=/opt/miniconda-latest/envs/neuro
-            docker run --rm -v /tmp/data/ds003_fmriprep:/data \
+            docker run --rm -v /tmp/data/fitlins_tests/ds003/ds003_fmriprep:/data:ro \
                 -v /tmp/ds003/derivatives:/out \
                 -v /tmp/ds003/work:/scratch \
-                -v /tmp/data/ds003_models:/models \
+                -v /tmp/data/fitlins_tests/ds003/models:/models \
                 -e COVERAGE_FILE=/scratch/.coverage.database-file-new \
                 --entrypoint="/neurodocker/startup.sh" \
                 poldracklab/fitlins:latest \
@@ -282,10 +276,10 @@ jobs:
           no_output_timeout: 2h
           command: |
             export CONDA_PREFIX=/opt/miniconda-latest/envs/neuro
-            docker run --rm -v /tmp/data/ds003_fmriprep:/data \
+            docker run --rm -v /tmp/data/fitlins_tests/ds003/ds003_fmriprep:/data:ro \
                 -v /tmp/ds003/derivatives:/out \
                 -v /tmp/ds003/work:/scratch \
-                -v /tmp/data/ds003_models:/models \
+                -v /tmp/data/fitlins_tests/ds003/models:/models \
                 -e COVERAGE_FILE=/scratch/.coverage.database-file-exists \
                 --entrypoint="/neurodocker/startup.sh" \
                 poldracklab/fitlins:latest \
@@ -484,10 +478,10 @@ workflows:
             tags:
               only: /.*/
       - test_ds003:
-          name: test_ds003_<< matrix.estimator >>
+          name: test_ds003_<< matrix.test_name >>
           matrix:
             parameters:
-              estimator: ["afni", "nistats"]
+              test_name: ["afni_smooth", "nistats_smooth", "afni_blurto", "nistats_blurto"]
           requires:
             - build
             - cache_test_data
@@ -506,15 +500,19 @@ workflows:
               only: /.*/
       - deploy_master:
           requires:
-            - test_ds003_nistats
-            - test_ds003_afni
+            - test_ds003_nistats_smooth
+            - test_ds003_nistats_blurto
+            - test_ds003_afni_smooth
+            - test_ds003_afni_blurto
           filters:
             branches:
               only: master
       - deploy_docker:
           requires:
-            - test_ds003_nistats
-            - test_ds003_afni
+            - test_ds003_nistats_smooth
+            - test_ds003_nistats_blurto
+            - test_ds003_afni_smooth
+            - test_ds003_afni_blurto
             - build_docs
           filters:
             branches:
@@ -523,8 +521,10 @@ workflows:
               only: /.*/
       - deploy_pypi:
           requires:
-            - test_ds003_nistats
-            - test_ds003_afni
+            - test_ds003_nistats_smooth
+            - test_ds003_nistats_blurto
+            - test_ds003_afni_smooth
+            - test_ds003_afni_blurto
             - build_docs
             - test_packaging
           filters:

fitlins/cli/run.py

@@ -112,7 +112,10 @@ def get_parser():
                              "Optional analysis LEVEL (default: l1) may be specified numerically "
                              "(e.g., `l1`) or by name (`run`, `subject`, `session` or `dataset`). "
                              "Optional smoothing TYPE (default: iso) must be one of:  "
-                             " `iso` (isotropic). e.g., `--smoothing 5:dataset:iso` will perform "
+                             " `iso` (isotropic additive smoothing), `isoblurto` (isotropic "
+                             "smoothing progressivley applied till "
+                             "the target smoothness is reached). "
+                             "e.g., `--smoothing 5:dataset:iso` will perform "
                              "a 5mm FWHM isotropic smoothing on subject-level maps, "
                              "before evaluating the dataset level.")
 
@@ -140,7 +143,7 @@ def get_parser():
                          default=None, choices=["polynomial", "cosine", None])
     g_other.add_argument("--error-ts", action='store_true', default=False,
                          help='save error time series for first level models.'
-                        ' Currently only implemented for afni estimator.')
+                         ' Currently only implemented for afni estimator.')
 
     return parser
 
@@ -162,7 +165,6 @@ def run_fitlins(argv=None):
         # Iterate over empty tuple if undefined
         for ign in opts.ignore or ()]
 
-
     log_level = 25 + 5 * (opts.quiet - opts.verbose)
     logger.setLevel(log_level)
     nlogging.getLogger('nipype.workflow').setLevel(log_level)
@@ -204,18 +206,20 @@ def run_fitlins(argv=None):
         # TODO - fix neuroscout
         derivatives = derivatives[0].split(" ")
 
-    if opts.error_ts and opts.estimator != 'afni':
-        raise NotImplementedError("Saving the error time series is only implmented for"
-                                  " the afni estimator. If this is a feature you want"
-                                  f" for {opts.estimator} please let us know on github.")
+    if opts.estimator != 'afni':
+        if opts.error_ts:
+            raise NotImplementedError("Saving the error time series is only implmented for"
+                                      " the afni estimator. If this is a feature you want"
+                                      f" for {opts.estimator} please let us know on github.")
 
     pipeline_name = 'fitlins'
     if opts.derivative_label:
         pipeline_name += '_' + opts.derivative_label
     deriv_dir = op.join(opts.output_dir, pipeline_name)
     os.makedirs(deriv_dir, exist_ok=True)
     fub.write_derivative_description(
-        opts.bids_dir, deriv_dir, vars(opts))
+        opts.bids_dir, deriv_dir, vars(opts)
+    )
 
     work_dir = mkdtemp() if opts.work_dir is None else opts.work_dir
 

fitlins/interfaces/abstract.py

@@ -37,6 +37,7 @@ class FirstLevelEstimatorInputSpec(TraitedSpec):
     design_matrix = File(exists=True, mandatory=True)
     contrast_info = traits.List(traits.Dict)
     smoothing_fwhm = traits.Float(desc='Full-width half max (FWHM) in mm for smoothing in mask')
+    smoothing_type = traits.Enum('iso', 'isoblurto', desc='Type of smoothing (iso or isoblurto)')
 
 
 class EstimatorOutputSpec(TraitedSpec):
@@ -61,6 +62,7 @@ class SecondLevelEstimatorInputSpec(TraitedSpec):
     stat_metadata = traits.List(traits.List(traits.Dict), mandatory=True)
     contrast_info = traits.List(traits.Dict, mandatory=True)
     smoothing_fwhm = traits.Float(desc='Full-width half max (FWHM) in mm for smoothing in mask')
+    smoothing_type = traits.Enum('iso', 'isoblurto', desc='Type of smoothing (iso or isoblurto)')
 
 
 class SecondLevelEstimatorOutputSpec(EstimatorOutputSpec):