diff --git a/CPAC/anat_preproc/ants.py b/CPAC/anat_preproc/ants.py index 9ad40faf4e..89222d4ce7 100644 --- a/CPAC/anat_preproc/ants.py +++ b/CPAC/anat_preproc/ants.py @@ -17,7 +17,7 @@ from packaging.version import parse as parseversion, Version # nipype -from nipype.pipeline import engine as pe +from CPAC.pipeline.nipype_pipeline_engine import engine as pe from nipype.interfaces import utility as niu from nipype.interfaces.fsl.maths import ApplyMask from nipype.interfaces.ants import N4BiasFieldCorrection, Atropos, MultiplyImages diff --git a/CPAC/pipeline/nipype_pipeline_engine/__init__.py b/CPAC/pipeline/nipype_pipeline_engine/__init__.py index ffec3b6269..f84383fda4 100644 --- a/CPAC/pipeline/nipype_pipeline_engine/__init__.py +++ b/CPAC/pipeline/nipype_pipeline_engine/__init__.py @@ -4,9 +4,9 @@ See https://nipype.readthedocs.io/en/latest/api/generated/nipype.pipeline.engine.html for Nipype's documentation.''' # noqa E501 from nipype.pipeline import engine as pe -# import __all__ from nipype.pipeline.engine +# import everything in nipype.pipeline.engine.__all__ from nipype.pipeline.engine import * # noqa F401 -# import DEFAULT_MEM_GB and override Node, MapNode +# import our DEFAULT_MEM_GB and override Node, MapNode from .engine import DEFAULT_MEM_GB, Node, MapNode __all__ = [ diff --git a/CPAC/registration/registration.py b/CPAC/registration/registration.py index e925da6bc4..af4c296c50 100644 --- a/CPAC/registration/registration.py +++ b/CPAC/registration/registration.py @@ -2272,7 +2272,8 @@ def warp_timeseries_to_T1template(wf, cfg, strat_pool, pipe_num, opt=None): apply_xfm = apply_transform(f'warp_ts_to_T1template_{pipe_num}', reg_tool, time_series=True, num_cpus=num_cpus, - num_ants_cores=num_ants_cores) + num_ants_cores=num_ants_cores, + mem_gb=2.5) if reg_tool == 'ants': apply_xfm.inputs.inputspec.interpolation = cfg.registration_workflows[ @@ -2486,9 +2487,10 @@ def warp_timeseries_to_EPItemplate(wf, cfg, strat_pool, pipe_num, opt=None): num_ants_cores = cfg.pipeline_setup['system_config']['num_ants_threads'] - apply_xfm = apply_transform('warp_ts_to_EPItemplate', reg_tool, + apply_xfm = apply_transform(f'warp_ts_to_EPItemplate_{pipe_num}', reg_tool, time_series=True, num_cpus=num_cpus, - num_ants_cores=num_ants_cores) + num_ants_cores=num_ants_cores, + mem_gb=2.5) if reg_tool == 'ants': apply_xfm.inputs.inputspec.interpolation = cfg.registration_workflows[ diff --git a/CPAC/seg_preproc/seg_preproc.py b/CPAC/seg_preproc/seg_preproc.py index 89b5455552..ceaa30acb5 100644 --- a/CPAC/seg_preproc/seg_preproc.py +++ b/CPAC/seg_preproc/seg_preproc.py @@ -575,8 +575,7 @@ def tissue_seg_fsl_fast(wf, cfg, strat_pool, pipe_num, opt=None): # 'probability_maps' output is a list of individual probability maps # triggered by 'probability_maps' boolean input (-p) - segment = pe.Node(interface=fsl.FAST(), name=f'segment_{pipe_num}', - mem_gb=1.5) + segment = pe.Node(interface=fsl.FAST(), name=f'segment_{pipe_num}') segment.inputs.img_type = 1 segment.inputs.segments = True segment.inputs.probability_maps = True diff --git a/CPAC/vmhc/vmhc.py b/CPAC/vmhc/vmhc.py index fe2b0d8123..0aa5db6497 100644 --- a/CPAC/vmhc/vmhc.py +++ b/CPAC/vmhc/vmhc.py @@ -81,7 +81,8 @@ def warp_timeseries_to_sym_template(wf, cfg, strat_pool, pipe_num, opt=None): apply_xfm = apply_transform(f'warp_ts_to_sym_template_{pipe_num}', reg_tool, time_series=True, num_cpus=num_cpus, - num_ants_cores=num_ants_cores) + num_ants_cores=num_ants_cores, + mem_gb=2.5) if reg_tool == 'ants': apply_xfm.inputs.inputspec.interpolation = cfg.registration_workflows[