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Merge pull request #50 from CoBrALab/updates
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Added memory specification for running in multiproc.
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Gab-D-G authored Jan 20, 2020
2 parents 0581aa6 + 88738fb commit 1d87685
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Showing 3 changed files with 6 additions and 6 deletions.
2 changes: 1 addition & 1 deletion rabies/preprocess_bold_pkg/hmc.py
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ def init_bold_hmc_wf(name='bold_hmc_wf'):
name='outputnode')

# Head motion correction (hmc)
motion_estimation = pe.Node(EstimateMotion(), name='ants_MC')
motion_estimation = pe.Node(EstimateMotion(), name='ants_MC', mem_gb=3)
motion_estimation.plugin_args = {'qsub_args': '-pe smp 4', 'overwrite': True}


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2 changes: 1 addition & 1 deletion rabies/preprocess_bold_pkg/registration.py
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ def init_bold_reg_wf(coreg_script='SyN', name='bold_reg_wf'):
run_reg = pe.Node(Function(input_names=["reg_script", "moving_image", "fixed_image",
"anat_mask"],
output_names=['affine_bold2anat', 'warp_bold2anat', 'inverse_warp_bold2anat', 'output_warped_bold'],
function=run_antsRegistration), name='EPI_Coregistration')
function=run_antsRegistration), name='EPI_Coregistration', mem_gb=3)
run_reg.inputs.reg_script=coreg_script
run_reg.plugin_args = {'qsub_args': '-pe smp 4', 'overwrite': True}

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8 changes: 4 additions & 4 deletions rabies/preprocess_bold_pkg/resampling.py
Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,12 @@ def init_bold_preproc_trans_wf(resampling_dim, name='bold_preproc_trans_wf'):
name='outputnode')


bold_transform = pe.Node(slice_applyTransforms(), name='bold_transform')
bold_transform = pe.Node(slice_applyTransforms(), name='bold_transform', mem_gb=3)
bold_transform.inputs.apply_motcorr = True
bold_transform.inputs.resampling_dim = resampling_dim
bold_transform.inputs.data_type = os.environ["rabies_data_type"]

merge = pe.Node(Merge(), name='merge')
merge = pe.Node(Merge(), name='merge', mem_gb=3)
merge.inputs.data_type = os.environ["rabies_data_type"]
#merge.plugin_args = {'qsub_args': '-pe smp 2 -l h_vmem=1G ', 'overwrite': True}

Expand Down Expand Up @@ -66,13 +66,13 @@ def init_bold_commonspace_trans_wf(resampling_dim, name='bold_commonspace_trans_
niu.IdentityInterface(fields=['bold', 'bold_ref', 'brain_mask', 'WM_mask', 'CSF_mask', 'labels']),
name='outputnode')

bold_transform = pe.Node(slice_applyTransforms(), name='bold_transform')
bold_transform = pe.Node(slice_applyTransforms(), name='bold_transform', mem_gb=3)
bold_transform.inputs.apply_motcorr = True
bold_transform.inputs.ref_file = os.environ["template_anat"]
bold_transform.inputs.resampling_dim = resampling_dim
bold_transform.inputs.data_type = os.environ["rabies_data_type"]

merge = pe.Node(Merge(), name='merge')
merge = pe.Node(Merge(), name='merge', mem_gb=3)
merge.inputs.data_type = os.environ["rabies_data_type"]

# Generate a new BOLD reference
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