From 54efc6ade4fb3821f39ab2c732a65d3a0b3360a9 Mon Sep 17 00:00:00 2001 From: mnoergaard Date: Mon, 8 Dec 2025 13:13:01 +0100 Subject: [PATCH 1/2] FIX: Fix parallel execution for mri_robust_template --- petprep/workflows/pet/hmc.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/petprep/workflows/pet/hmc.py b/petprep/workflows/pet/hmc.py index 1f60bb99..df51db91 100644 --- a/petprep/workflows/pet/hmc.py +++ b/petprep/workflows/pet/hmc.py @@ -237,6 +237,9 @@ def init_pet_hmc_wf( inputnode.inputs.frame_start_times = frame_start_times outputnode = pe.Node(niu.IdentityInterface(fields=['xforms', 'petref']), name='outputnode') + robust_template_threads = min(omp_nthreads, 4) + robust_template_mem_gb = min(mem_gb, 24) + # Split frames split = pe.Node(fs.MRIConvert(out_type='niigz', split=True), name='split_frames') @@ -313,11 +316,13 @@ def num_files(filelist): intensity_scaling=True, average_metric='mean', args='--cras', - num_threads=omp_nthreads, + num_threads=robust_template_threads, fixed_timepoint=fixed_frame, no_iteration=fixed_frame, ), name='est_robust_hmc', + n_procs=robust_template_threads, + mem_gb=robust_template_mem_gb, ) if not auto_init_frame: robust_template.inputs.initial_timepoint = int(initial_frame) + 1 From fdef7024179d39069a9177efad1630f0b1fe4b5c Mon Sep 17 00:00:00 2001 From: mnoergaard Date: Mon, 8 Dec 2025 13:14:11 +0100 Subject: [PATCH 2/2] FIX: update mem cap --- petprep/workflows/pet/hmc.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/petprep/workflows/pet/hmc.py b/petprep/workflows/pet/hmc.py index df51db91..e325fbdf 100644 --- a/petprep/workflows/pet/hmc.py +++ b/petprep/workflows/pet/hmc.py @@ -238,7 +238,7 @@ def init_pet_hmc_wf( outputnode = pe.Node(niu.IdentityInterface(fields=['xforms', 'petref']), name='outputnode') robust_template_threads = min(omp_nthreads, 4) - robust_template_mem_gb = min(mem_gb, 24) + robust_template_mem_gb = min(mem_gb, 16) # Split frames split = pe.Node(fs.MRIConvert(out_type='niigz', split=True), name='split_frames')