Merge branch 'develop' into fix/rbc_atlas_2mm

Author: sgiavasis

.github/Dockerfiles/C-PAC.develop-ABCD-HCP-bionic.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.4
+FROM ghcr.io/fcp-indi/c-pac/stage-base:abcd-hcp-v1.8.5.dev
 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [ABCD-HCP BIDS fMRI Pipeline](https://github.com/DCAN-Labs/abcd-hcp-pipeline/blob/e480a8f99534f1b05f37bf44c64827384b69b383/Dockerfile)"
 USER root
 

.github/Dockerfiles/C-PAC.develop-bionic.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.4
+FROM ghcr.io/fcp-indi/c-pac/stage-base:standard-v1.8.5.dev
 LABEL org.opencontainers.image.description "Full C-PAC image"
 USER root
 

.github/Dockerfiles/C-PAC.develop-fMRIPrep-LTS-xenial.Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.4
+FROM ghcr.io/fcp-indi/c-pac/stage-base:fmriprep-lts-v1.8.5.dev
 LABEL org.opencontainers.image.description "Full C-PAC image with software dependencies version-matched to [fMRIPrep LTS](https://reproducibility.stanford.edu/fmriprep-lts#long-term-support-lts)"
 USER root
 

.github/Dockerfiles/Ubuntu.bionic-non-free.Dockerfile

@@ -1,5 +1,7 @@
+FROM ghcr.io/fcp-indi/c-pac_templates:latest as c-pac_templates
 FROM neurodebian:bionic-non-free AS dcan-hcp
 
+
 ARG DEBIAN_FRONTEND=noninteractive
 
 # Adding DCAN dependencies & HCP code
@@ -145,10 +147,15 @@ RUN conda update conda -y && \
     git lfs install
 
 # Installing C-PAC templates and atlases
-COPY --from=ghcr.io/fcp-indi/c-pac_templates:latest /cpac_templates /cpac_templates
+COPY --from=c-pac_templates /cpac_templates /cpac_templates
 COPY --from=dcan-hcp /opt/dcan-tools/pipeline/global /opt/dcan-tools/pipeline/global
 COPY --from=ghcr.io/fcp-indi/c-pac/neuroparc:v1.0-human /ndmg_atlases /ndmg_atlases
 
+# Installing surface files for downsampling
+COPY --from=c-pac_templates /opt/dcan-tools/pipeline/global/templates/standard_mesh_atlases/ /opt/dcan-tools/pipeline/global/templates/standard_mesh_atlases/
+COPY --from=c-pac_templates /opt/dcan-tools/pipeline/global/templates/Greyordinates/ /opt/dcan-tools/pipeline/global/templates/Greyordinates/
+
+
 ENTRYPOINT ["/bin/bash"]
 
 # Link libraries for Singularity images

.github/Dockerfiles/Ubuntu.xenial-20200114.Dockerfile

@@ -1,3 +1,4 @@
+FROM ghcr.io/fcp-indi/c-pac_templates:latest as c-pac_templates
 FROM nipreps/fmriprep:20.2.1 as fmriprep
 FROM ubuntu:xenial-20200114 AS dcan-hcp
 
@@ -156,9 +157,13 @@ RUN pip install -r /opt/requirements.txt
 RUN pip install xvfbwrapper
 
 # install cpac templates
-COPY --from=ghcr.io/fcp-indi/c-pac_templates:latest /cpac_templates /cpac_templates
+COPY --from=c-pac_templates /cpac_templates /cpac_templates
 COPY --from=dcan-hcp /opt/dcan-tools/pipeline/global /opt/dcan-tools/pipeline/global
 
+# Installing surface files for downsampling
+COPY --from=c-pac_templates /opt/dcan-tools/pipeline/global/templates/standard_mesh_atlases/ /opt/dcan-tools/pipeline/global/templates/standard_mesh_atlases/
+COPY --from=c-pac_templates /opt/dcan-tools/pipeline/global/templates/Greyordinates/ /opt/dcan-tools/pipeline/global/templates/Greyordinates/
+
 RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash
 RUN apt-get install git-lfs
 RUN git lfs install

CHANGELOG.md

@@ -14,11 +14,16 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## unreleased
+## [v1.8.5]
+
+### Added
+- Added the ability to downsample to 10K or 2K resolution for freesurfer runs
 
 ### Changed
 - Changed the 1mm atlases chosen in the rbc-options preconfig to the 2mm versions
 
+### Fixed
+
 ## [v1.8.4] - 2022-06-27
 
 ### Added

CPAC/func_preproc/func_preproc.py

@@ -574,7 +574,7 @@ def get_idx(in_files, stop_idx=None, start_idx=None):
     else:
         startidx = int(start_idx)
 
-    if (stop_idx == None) or (int(stop_idx) > (nvols - 1)):
+    if (stop_idx in [None, "End"]) or (int(stop_idx) > (nvols - 1)):
         stopidx = nvols - 1
     else:
         stopidx = int(stop_idx)

CPAC/pipeline/schema.py

@@ -20,7 +20,7 @@
 from itertools import chain, permutations
 
 import numpy as np
-from voluptuous import All, ALLOW_EXTRA, Any, In, Length, Match, Optional, \
+from voluptuous import All, Capitalize, ALLOW_EXTRA, Any, In, Length, Match, Optional, \
                        Range, Required, Schema
 from voluptuous.validators import ExactSequence, Maybe
 
@@ -749,7 +749,7 @@ def _changes_1_8_0_to_1_8_1(config_dict):
         'run': bool,
         'truncation': {
             'start_tr': int,
-            'stop_tr': Maybe(Any(int, 'End'))
+            'stop_tr': Maybe(Any(int, All(Capitalize, 'End')))
         },
         'scaling': {
             'run': bool,

CPAC/surface/surf_preproc.py

@@ -40,6 +40,7 @@ def run_surface(post_freesurfer_folder,
     import subprocess
 
     freesurfer_folder = os.path.join(freesurfer_folder, 'recon_all')
+    
 
     # DCAN-HCP PostFreeSurfer
     # Ref: https://github.com/DCAN-Labs/DCAN-HCP/blob/master/PostFreeSurfer/PostFreeSurferPipeline.sh
@@ -111,6 +112,7 @@ def surface_connector(wf, cfg, strat_pool, pipe_num, opt):
                                  function=run_surface),
                    name=f'post_freesurfer_{pipe_num}')
 
+    
     surf.inputs.subject = cfg['subject_id']
 
     surf.inputs.post_freesurfer_folder = os.path.join(cfg.pipeline_setup['working_directory']['path'],
@@ -141,10 +143,12 @@ def surface_connector(wf, cfg, strat_pool, pipe_num, opt):
 
     node, out = strat_pool.get_data('freesurfer-subject-dir')
     wf.connect(node, out, surf, 'freesurfer_folder')
+    
 
     node, out = strat_pool.get_data(restore) 
     wf.connect(node, out, surf, 't1w_restore_image')
-
+    
+    
     node, out = strat_pool.get_data(space_temp) 
     wf.connect(node, out, surf, 'atlas_space_t1w_image')
 

CPAC/surface/tests/test_config.py

@@ -9,7 +9,7 @@
 from CPAC.pipeline.cpac_pipeline import run_workflow
 from CPAC.utils.configuration import Configuration
 
-
+@pytest.mark.skip(reason='timing out for unrelated reasons')
 @pytest.mark.timeout(60)
 def test_duplicate_freesurfer(tmp_path):
     """The pipeline should build fast if freesurfer is not self-duplicating"""