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FIX: Address memory issues in DWI pipeline #1323

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merged 1 commit into from
Aug 18, 2024
Merged

FIX: Address memory issues in DWI pipeline #1323

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24 changes: 12 additions & 12 deletions mriqc/workflows/diffusion/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,21 +131,21 @@ def dmri_qc_workflow(name='dwiMRIQC'):
get_lowb = pe.Node(
ExtractOrientations(),
name='get_lowb',
n_procs=max(1, config.nipype.omp_nthreads // 2),
n_procs=max(1, config.nipype.nprocs // 2),
)

# Generate B0 reference
dwi_ref = pe.Node(
RobustAverage(mc_method=None),
name='dwi_ref',
n_procs=max(1, config.nipype.omp_nthreads // 2),
n_procs=max(1, config.nipype.nprocs // 2),
)

hmc_b0 = pe.Node(
Volreg(args='-Fourier -twopass', zpad=4, outputtype='NIFTI_GZ'),
name='hmc_b0',
mem_gb=3.0,
n_procs=config.nipype.omp_nthreads,
n_procs=config.nipype.nprocs,
)

# Calculate brainmask
Expand All @@ -164,13 +164,13 @@ def dmri_qc_workflow(name='dwiMRIQC'):
averages = pe.MapNode(
WeightedStat(),
name='averages',
n_procs=max(1, config.nipype.omp_nthreads // 2),
n_procs=max(1, config.nipype.nprocs // 2),
iterfield=['in_weights'],
)
stddev = pe.MapNode(
WeightedStat(stat='std'),
name='stddev',
n_procs=max(1, config.nipype.omp_nthreads // 2),
n_procs=max(1, config.nipype.nprocs // 2),
iterfield=['in_weights'],
)

Expand All @@ -180,38 +180,38 @@ def dmri_qc_workflow(name='dwiMRIQC'):
nthreads=config.nipype.omp_nthreads,
),
name='dwidenoise',
n_procs=config.nipype.omp_nthreads,
n_procs=config.nipype.nprocs,
)
drift = pe.Node(
CorrectSignalDrift(),
name='drift',
n_procs=max(1, config.nipype.omp_nthreads // 2),
n_procs=max(1, config.nipype.nprocs // 2),
)
sp_mask = pe.Node(
SpikingVoxelsMask(),
name='sp_mask',
n_procs=max(1, config.nipype.omp_nthreads // 2),
n_procs=max(1, config.nipype.nprocs // 2),
)

# Fit DTI/DKI model
dwimodel = pe.Node(
DiffusionModel(),
name='dwimodel',
n_procs=max(1, config.nipype.omp_nthreads // 2),
n_procs=config.nipype.nprocs,
)

# Calculate CC mask
cc_mask = pe.Node(
CCSegmentation(),
name='cc_mask',
n_procs=max(1, config.nipype.omp_nthreads // 2),
n_procs=max(1, config.nipype.nprocs // 2),
)

# Run PIESNO noise estimation
piesno = pe.Node(
PIESNO(),
name='piesno',
n_procs=max(1, config.nipype.omp_nthreads // 2),
n_procs=max(1, config.nipype.nprocs // 2),
)

# EPI to MNI registration
Expand Down Expand Up @@ -483,7 +483,7 @@ def hmc_workflow(name='dMRI_HMC'):
Volreg(args='-Fourier -twopass', zpad=4, outputtype='NIFTI_GZ'),
name='motion_correct',
mem_gb=3.0,
n_procs=config.nipype.omp_nthreads,
n_procs=config.nipype.nprocs,
)

bvec_rot = pe.Node(RotateVectors(), name='bvec_rot')
Expand Down
5 changes: 5 additions & 0 deletions mriqc/workflows/diffusion/output.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,10 +81,12 @@ def init_dwi_report_wf(name='dwi_report_wf'):
mosaic_fa = pe.Node(
PlotMosaic(cmap='Greys_r'),
name='mosaic_fa',
n_procs=max(1, config.nipype.nprocs // 2),
)
mosaic_md = pe.Node(
PlotMosaic(cmap='Greys_r'),
name='mosaic_md',
n_procs=max(1, config.nipype.nprocs // 2),
)

mosaic_snr = pe.MapNode(
Expand All @@ -97,6 +99,7 @@ def init_dwi_report_wf(name='dwi_report_wf'):
),
name='mosaic_snr',
iterfield=['before', 'after'],
n_procs=max(1, config.nipype.nprocs // 2),
)

mosaic_noise = pe.MapNode(
Expand All @@ -106,6 +109,7 @@ def init_dwi_report_wf(name='dwi_report_wf'):
),
name='mosaic_noise',
iterfield=['in_file'],
n_procs=max(1, config.nipype.nprocs // 2),
)

if config.workflow.species.lower() in ('rat', 'mouse'):
Expand Down Expand Up @@ -187,6 +191,7 @@ def _gen_entity(inlist):
plot_heatmap = pe.Node(
DWIHeatmap(scalarmap_label='Shell-wise Fractional Anisotropy (FA)'),
name='plot_heatmap',
n_procs=config.nipype.nprocs,
)
ds_report_hm = pe.Node(
DerivativesDataSink(
Expand Down
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