From 877ad21577a2e4c6db7cb34408b810d9a8ba7b9b Mon Sep 17 00:00:00 2001 From: Dylan Nielson Date: Wed, 13 Dec 2023 09:45:55 -0500 Subject: [PATCH] update notebooks --- notebooks/generate_and_evaluate_targets.ipynb | 100 ++++----- notebooks/prep_normgrid_targeting.ipynb | 199 ++++++++++++++---- notebooks/run_liston_lab_pipeline.ipynb | 30 +-- 3 files changed, 220 insertions(+), 109 deletions(-) diff --git a/notebooks/generate_and_evaluate_targets.ipynb b/notebooks/generate_and_evaluate_targets.ipynb index 0e740d3..247a987 100644 --- a/notebooks/generate_and_evaluate_targets.ipynb +++ b/notebooks/generate_and_evaluate_targets.ipynb @@ -4151,11 +4151,11 @@ "text": [ "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866028582 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.6 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866028902 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866029227 (866 million) bytes long!\n", @@ -4168,11 +4168,11 @@ "++ elapsed time = 3.9 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866030175 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.6 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866030498 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.9 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866030826 (866 million) bytes long!\n", @@ -4185,11 +4185,11 @@ "++ elapsed time = 3.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866031783 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.6 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866032106 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866032434 (866 million) bytes long!\n", @@ -4202,11 +4202,11 @@ "++ elapsed time = 3.9 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866033391 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866033711 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866034036 (866 million) bytes long!\n", @@ -4219,11 +4219,11 @@ "++ elapsed time = 4.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866034984 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866035304 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866035629 (866 million) bytes long!\n", @@ -4236,11 +4236,11 @@ "++ elapsed time = 4.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866036577 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.7 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866036897 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866037222 (866 million) bytes long!\n", @@ -4253,11 +4253,11 @@ "++ elapsed time = 4.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866038170 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866038490 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.8 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866038815 (866 million) bytes long!\n", @@ -4270,11 +4270,11 @@ "++ elapsed time = 4.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866039763 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.1 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866040086 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.4 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866040414 (866 million) bytes long!\n", @@ -4287,11 +4287,11 @@ "++ elapsed time = 3.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866041371 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866041691 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.4 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866042016 (866 million) bytes long!\n", @@ -4304,11 +4304,11 @@ "++ elapsed time = 2.9 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866042964 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.3 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866043284 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 0.9 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866043609 (866 million) bytes long!\n", @@ -5852,53 +5852,53 @@ "++ WARNING: file /home/nielsond/.afni.log is now 866057943 (866 million) bytes long!\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866058271 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866058602 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866058930 (866 million) bytes long!\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866059261 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866059589 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866059917 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866060245 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866060573 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866060901 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.5 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866061232 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.3 s\n", "++ elapsed time = 2.4 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866061558 (866 million) bytes long!\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866061884 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.9 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866062213 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.9 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866062542 (866 million) bytes long!\n", "++ elapsed time = 3.1 s\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866062868 (866 million) bytes long!\n", "++ elapsed time = 3.2 s\n", @@ -5906,61 +5906,61 @@ "++ elapsed time = 3.2 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866063194 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.9 s\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866063520 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866063846 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866064172 (866 million) bytes long!\n", "++ elapsed time = 1.5 s\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866064501 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 1.0 s\n", "++ elapsed time = 2.2 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866064854 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.3 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866065207 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.9 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866065563 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.9 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866065919 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.9 s\n", "++ elapsed time = 1.5 s\n", "++ elapsed time = 3.1 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866066272 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866066628 (866 million) bytes long!\n", "++ elapsed time = 1.5 s\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 3.1 s\n", "++ elapsed time = 3.1 s\n", "++ elapsed time = 3.1 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866066981 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866067334 (866 million) bytes long!\n", "++ 3dTcat: AFNI version=AFNI_23.3.09 (Nov 22 2023) [64-bit]\n", "++ WARNING: file /home/nielsond/.afni.log is now 866067687 (866 million) bytes long!\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", - "\u001b[7m*+ WARNING:\u001b[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", + "\u001B[7m*+ WARNING:\u001B[0m Set TR of output dataset to 1.0 s\n", "++ elapsed time = 2.1 s\n", "++ elapsed time = 2.1 s\n", "++ elapsed time = 2.1 s\n", diff --git a/notebooks/prep_normgrid_targeting.ipynb b/notebooks/prep_normgrid_targeting.ipynb index 973b1c7..1187b1d 100644 --- a/notebooks/prep_normgrid_targeting.ipynb +++ b/notebooks/prep_normgrid_targeting.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 27, + "execution_count": 22, "id": "7e2f7ed6-0931-427d-99bd-b6f86b9145a8", "metadata": { "tags": [] @@ -10,15 +10,23 @@ "outputs": [], "source": [ "from pathlib import Path\n", + "from pkg_resources import resource_filename\n", "from joblib import Parallel, delayed\n", "\n", - "from contarg.utils import load_timeseries\n", - "from contarg.normgrid import get_prob_vine, setup_uncert_sims, run_clusters, calc_stimgrid" + "import numpy as np\n", + "import pandas as pd\n", + "from contarg.normgrid import (\n", + " get_prob_vine,\n", + " setup_uncert_sims,\n", + " run_clusters,\n", + " calc_stimgrid,\n", + " make_uncert_sims\n", + ")" ] }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 6, "id": "c2262a91-7255-40b3-8066-f34035b3e7ff", "metadata": { "tags": [] @@ -52,6 +60,8 @@ "\n", "outdir = Path('/data/EDB/TMSpilot/derivatives/contarg_liston_ohbm2024')\n", "outdir.mkdir(exist_ok=True)\n", + "anat_dir = outdir / 'anat_preproc'\n", + "\n", "jobids = {}\n", "\n", "liston_root = Path('/data/EDB/TMSpilot/liston')" @@ -92,7 +102,6 @@ "cmds = []\n", "for hmsub in subjects:\n", " session = 1\n", - " anat_dir = outdir / 'anat_preproc'\n", " ses_out_dir = anat_dir /f'sub-{hmsub}'\n", " ses_out_dir.mkdir(exist_ok=True, parents=True)\n", " proced_anat_dir = liston_root / f'sub-{hmsub}/anat'\n", @@ -194,6 +203,10 @@ "execution_count": 28, "id": "fa309da7-8232-47ca-9d0a-cddfe690264d", "metadata": { + "collapsed": true, + "jupyter": { + "outputs_hidden": true + }, "tags": [] }, "outputs": [ @@ -510,6 +523,9 @@ "execution_count": 29, "id": "75b37f37-6385-499e-9b3c-62412bf27ea8", "metadata": { + "jupyter": { + "source_hidden": true + }, "tags": [] }, "outputs": [], @@ -541,7 +557,7 @@ }, { "cell_type": "code", - "execution_count": 30, + "execution_count": 31, "id": "ccade262-d623-4e38-a5ca-35e955283301", "metadata": { "tags": [] @@ -599,13 +615,11 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "id": "4a0393a2-fe42-4a7f-83a3-e5cb658218b9", "metadata": {}, "outputs": [], "source": [ - "anat_dir = Path('/data/EDB/TMSpilot/derivatives/contarg_liston/anat_preproc/')\n", - "\n", "\n", "coil='MagVenture_MCF-B65.ccd'\n", "\n", @@ -622,7 +636,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 14, "id": "0c7058bf-1d14-4a7d-85c1-8a81c4f1c022", "metadata": {}, "outputs": [], @@ -637,7 +651,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 16, "id": "8f332b9f-92e2-4eca-91d2-c39f0368abbf", "metadata": {}, "outputs": [], @@ -657,17 +671,32 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "id": "5a3e2e0b-31d0-46cd-a149-b923b6fab5d0", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[Parallel(n_jobs=8)]: Using backend LokyBackend with 8 concurrent workers.\n", + "[Parallel(n_jobs=8)]: Done 1 tasks | elapsed: 6.9min\n", + "[Parallel(n_jobs=8)]: Done 2 out of 7 | elapsed: 8.2min remaining: 20.5min\n", + "[Parallel(n_jobs=8)]: Done 3 out of 7 | elapsed: 8.2min remaining: 11.0min\n", + "[Parallel(n_jobs=8)]: Done 4 out of 7 | elapsed: 8.4min remaining: 6.3min\n", + "[Parallel(n_jobs=8)]: Done 5 out of 7 | elapsed: 8.8min remaining: 3.5min\n", + "[Parallel(n_jobs=8)]: Done 7 out of 7 | elapsed: 10.7min remaining: 0.0s\n", + "[Parallel(n_jobs=8)]: Done 7 out of 7 | elapsed: 10.7min finished\n" + ] + } + ], "source": [ "all_settings = Parallel(n_jobs=8, verbose=10)(jobs)" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 23, "id": "d26ea3c0-524b-4556-b9c0-8c64244c13b0", "metadata": {}, "outputs": [], @@ -709,17 +738,107 @@ " '--out-dir',\n", " settings_path.parent.as_posix(),\n", " '--njobs',\n", - " f'20'\n", + " f'20',\n", + " '--thresh-type=mt',\n", + " '--min-thresh=50',\n", + " '--max-thresh=80',\n", + " '--max-mt=80',\n", " ]\n", " cmds.append(' '.join(cmd))" ] }, + { + "cell_type": "code", + "execution_count": 24, + "id": "9179d2aa-aa4a-40cd-9703-1d148e943717", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "'contarg normgrid sim-uncert --headmesh-path /data/EDB/TMSpilot/derivatives/contarg_liston_ohbm2024/anat_preproc/sub-24546/HeadModel/m2m_24546/24546.msh --settings-path /data/EDB/TMSpilot/derivatives/contarg_liston_ohbm2024/anat_preproc/sub-24546/Simulation/simulation-00/uncert1000/settings.pkl.gz --ix 0 --coil-path /gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/simnibs/resources/coil_models/Drakaki_BrainStim_2022/MagVenture_MCF-B65.ccd --tmp-dir /lscratch/$SLURM_JOB_ID/uncertsim-0 --out-dir /data/EDB/TMSpilot/derivatives/contarg_liston_ohbm2024/anat_preproc/sub-24546/Simulation/simulation-00/uncert1000 --njobs 20 --thresh-type=mt --min-thresh=50 --max-thresh=80 --max-mt=80'" + ] + }, + "execution_count": 24, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "cmds[0]" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "4da24ca1-db3f-4da1-bab3-48d128aea1e9", + "metadata": { + "tags": [] + }, + "outputs": [], + "source": [ + "!rm -rf /lscratch/$SLURM_JOB_ID/uncertsim-0" + ] + }, { "cell_type": "code", "execution_count": null, + "id": "b3a7af00-6223-4f66-b9d9-07beddcdcbc9", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "[Parallel(n_jobs=20)]: Using backend LokyBackend with 20 concurrent workers.\n" + ] + } + ], + "source": [ + "! {cmds[0]}" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "id": "7959e330-0f81-4248-a1e0-731837b851ab", + "metadata": { + "tags": [] + }, + "outputs": [ + { + "data": { + "text/plain": [ + "892" + ] + }, + "execution_count": 28, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "len(cmds)" + ] + }, + { + "cell_type": "code", + "execution_count": 32, "id": "9f035e6b-c51a-4efb-a695-68bff117e5d8", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "['14230167']\n" + ] + } + ], "source": [ "# deal with 1000 job swarm limit\n", "if len(cmds) > 0:\n", @@ -750,7 +869,8 @@ "id": "9b57c689-33ae-4bd2-b11c-66b2b18f1e15", "metadata": {}, "source": [ - "## Here's code for restarting failues" + "## Here's code for restarting failues\n", + "For currently unknown reasons, some jobs run slowly and time out. When rerun, those jobs complete without issue." ] }, { @@ -760,7 +880,17 @@ "metadata": {}, "outputs": [], "source": [ - "to_restart = [cmds[164], cmds[222], cmds[226], cmds[360]]\n", + "to_restart = [\n", + " cmds[428],\n", + " cmds[209],\n", + " cmds[185],\n", + " cmds[181],\n", + " cmds[137],\n", + " cmds[114],\n", + " cmds[45],\n", + " cmds[41],\n", + " cmds[35],\n", + "]\n", "to_restart" ] }, @@ -791,7 +921,7 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 3, "id": "e44bf5c2-e36a-418f-bc0d-3ab00d429344", "metadata": { "tags": [] @@ -827,7 +957,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": null, "id": "5b9cba6c-0a5b-4c5a-b5f8-243ea35e9f32", "metadata": { "tags": [] @@ -838,30 +968,11 @@ "output_type": "stream", "text": [ "[Parallel(n_jobs=20)]: Using backend LokyBackend with 20 concurrent workers.\n", - "[Parallel(n_jobs=20)]: Done 3 out of 14 | elapsed: 12.6s remaining: 46.3s\n", - "[Parallel(n_jobs=20)]: Done 5 out of 14 | elapsed: 13.1s remaining: 23.5s\n", - "[Parallel(n_jobs=20)]: Done 7 out of 14 | elapsed: 13.4s remaining: 13.4s\n", - "[Parallel(n_jobs=20)]: Done 9 out of 14 | elapsed: 13.9s remaining: 7.7s\n", - "[Parallel(n_jobs=20)]: Done 11 out of 14 | elapsed: 14.5s remaining: 3.9s\n" - ] - }, - { - "ename": "NameError", - "evalue": "name 'load_timeseries' is not defined", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31m_RemoteTraceback\u001b[0m Traceback (most recent call last)", - "\u001b[0;31m_RemoteTraceback\u001b[0m: \n\"\"\"\nTraceback (most recent call last):\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py\", line 428, in _process_worker\n r = call_item()\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py\", line 275, in __call__\n return self.fn(*self.args, **self.kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/_parallel_backends.py\", line 620, in __call__\n return self.func(*args, **kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py\", line 288, in __call__\n return [func(*args, **kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py\", line 288, in \n return [func(*args, **kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/contarg/contarg/normgrid.py\", line 1264, in run_clusters\n lts_data, rts_data, ts_data = load_timeseries(timeseries)\nNameError: name 'load_timeseries' is not defined\n\"\"\"", - "\nThe above exception was the direct cause of the following exception:\n", - "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[24], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m clustreses \u001b[38;5;241m=\u001b[39m \u001b[43mParallel\u001b[49m\u001b[43m(\u001b[49m\u001b[43mn_jobs\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m20\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mverbose\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m10\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m(\u001b[49m\u001b[43mjobs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py:1098\u001b[0m, in \u001b[0;36mParallel.__call__\u001b[0;34m(self, iterable)\u001b[0m\n\u001b[1;32m 1095\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_iterating \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m 1097\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_backend\u001b[38;5;241m.\u001b[39mretrieval_context():\n\u001b[0;32m-> 1098\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mretrieve\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1099\u001b[0m \u001b[38;5;66;03m# Make sure that we get a last message telling us we are done\u001b[39;00m\n\u001b[1;32m 1100\u001b[0m elapsed_time \u001b[38;5;241m=\u001b[39m time\u001b[38;5;241m.\u001b[39mtime() \u001b[38;5;241m-\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_start_time\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py:975\u001b[0m, in \u001b[0;36mParallel.retrieve\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 973\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 974\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_backend, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msupports_timeout\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m--> 975\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_output\u001b[38;5;241m.\u001b[39mextend(\u001b[43mjob\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m)\n\u001b[1;32m 976\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 977\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_output\u001b[38;5;241m.\u001b[39mextend(job\u001b[38;5;241m.\u001b[39mget())\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/_parallel_backends.py:567\u001b[0m, in \u001b[0;36mLokyBackend.wrap_future_result\u001b[0;34m(future, timeout)\u001b[0m\n\u001b[1;32m 564\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Wrapper for Future.result to implement the same behaviour as\u001b[39;00m\n\u001b[1;32m 565\u001b[0m \u001b[38;5;124;03mAsyncResults.get from multiprocessing.\"\"\"\u001b[39;00m\n\u001b[1;32m 566\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 567\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 568\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m CfTimeoutError \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 569\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01me\u001b[39;00m\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/concurrent/futures/_base.py:446\u001b[0m, in \u001b[0;36mFuture.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 444\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CancelledError()\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_state \u001b[38;5;241m==\u001b[39m FINISHED:\n\u001b[0;32m--> 446\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__get_result\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 447\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 448\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m()\n", - "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/concurrent/futures/_base.py:391\u001b[0m, in \u001b[0;36mFuture.__get_result\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 389\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception:\n\u001b[1;32m 390\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 391\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception\n\u001b[1;32m 392\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 393\u001b[0m \u001b[38;5;66;03m# Break a reference cycle with the exception in self._exception\u001b[39;00m\n\u001b[1;32m 394\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n", - "\u001b[0;31mNameError\u001b[0m: name 'load_timeseries' is not defined" + "[Parallel(n_jobs=20)]: Done 3 out of 14 | elapsed: 7.7min remaining: 28.1min\n", + "[Parallel(n_jobs=20)]: Done 5 out of 14 | elapsed: 9.2min remaining: 16.5min\n", + "[Parallel(n_jobs=20)]: Done 7 out of 14 | elapsed: 9.5min remaining: 9.5min\n", + "[Parallel(n_jobs=20)]: Done 9 out of 14 | elapsed: 10.7min remaining: 6.0min\n", + "[Parallel(n_jobs=20)]: Done 11 out of 14 | elapsed: 12.5min remaining: 3.4min\n" ] } ], diff --git a/notebooks/run_liston_lab_pipeline.ipynb b/notebooks/run_liston_lab_pipeline.ipynb index 4a93b9c..aab4d21 100644 --- a/notebooks/run_liston_lab_pipeline.ipynb +++ b/notebooks/run_liston_lab_pipeline.ipynb @@ -1210,10 +1210,10 @@ "evalue": "boolean index did not match indexed array along dimension 0; dimension is 2793 but corresponding boolean dimension is 2880", "output_type": "error", "traceback": [ - "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", - "\u001B[0;31mIndexError\u001B[0m Traceback (most recent call last)", - "Cell \u001B[0;32mIn[29], line 1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m \u001B[43mfd_mask\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mnonzero\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\u001B[43m[\u001B[49m\u001B[38;5;241;43m0\u001B[39;49m\u001B[43m]\u001B[49m\u001B[43m[\u001B[49m\u001B[43m(\u001B[49m\u001B[43mscanid\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43msession\u001B[49m\u001B[43m \u001B[49m\u001B[38;5;241;43m==\u001B[39;49m\u001B[43m \u001B[49m\u001B[43msession\u001B[49m\u001B[43m)\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mvalues\u001B[49m\u001B[43m]\u001B[49m\n", - "\u001B[0;31mIndexError\u001B[0m: boolean index did not match indexed array along dimension 0; dimension is 2793 but corresponding boolean dimension is 2880" + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mIndexError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[29], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mfd_mask\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mnonzero\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m[\u001b[49m\u001b[43m(\u001b[49m\u001b[43mscanid\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msession\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m==\u001b[39;49m\u001b[43m \u001b[49m\u001b[43msession\u001b[49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mvalues\u001b[49m\u001b[43m]\u001b[49m\n", + "\u001b[0;31mIndexError\u001b[0m: boolean index did not match indexed array along dimension 0; dimension is 2793 but corresponding boolean dimension is 2880" ] } ], @@ -29110,18 +29110,18 @@ "evalue": "Command '['wb_command', '-cifti-create-dense-timeseries', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii', '-volume', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz', '/data/MLDSST/nielsond/target_test/other_repos/HCPpipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz', '-left-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/lh.32k_fs_LR.shape.gii', '-roi-left', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.L.atlasroi.32k_fs_LR.shape.gii', '-right-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/rh.32k_fs_LR.shape.gii', '-roi-right', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.R.atlasroi.32k_fs_LR.shape.gii', '-timestep', '2.5']' returned non-zero exit status 255.", "output_type": "error", "traceback": [ - "\u001B[0;31m---------------------------------------------------------------------------\u001B[0m", - "\u001B[0;31m_RemoteTraceback\u001B[0m Traceback (most recent call last)", - "\u001B[0;31m_RemoteTraceback\u001B[0m: \n\"\"\"\nTraceback (most recent call last):\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py\", line 428, in _process_worker\n r = call_item()\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py\", line 275, in __call__\n return self.fn(*self.args, **self.kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/_parallel_backends.py\", line 620, in __call__\n return self.func(*args, **kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py\", line 288, in __call__\n return [func(*args, **kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py\", line 288, in \n return [func(*args, **kwargs)\n File \"/tmp/ipykernel_600570/1202779090.py\", line 117, in resample_procced_to_realfslr32\n File \"/tmp/ipykernel_600570/1202779090.py\", line 89, in create_fslr32k_sample\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/subprocess.py\", line 528, in run\n raise CalledProcessError(retcode, process.args,\nsubprocess.CalledProcessError: Command '['wb_command', '-cifti-create-dense-timeseries', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii', '-volume', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz', '/data/MLDSST/nielsond/target_test/other_repos/HCPpipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz', '-left-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/lh.32k_fs_LR.shape.gii', '-roi-left', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.L.atlasroi.32k_fs_LR.shape.gii', '-right-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/rh.32k_fs_LR.shape.gii', '-roi-right', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.R.atlasroi.32k_fs_LR.shape.gii', '-timestep', '2.5']' returned non-zero exit status 255.\n\"\"\"", + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31m_RemoteTraceback\u001b[0m Traceback (most recent call last)", + "\u001b[0;31m_RemoteTraceback\u001b[0m: \n\"\"\"\nTraceback (most recent call last):\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py\", line 428, in _process_worker\n r = call_item()\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py\", line 275, in __call__\n return self.fn(*self.args, **self.kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/_parallel_backends.py\", line 620, in __call__\n return self.func(*args, **kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py\", line 288, in __call__\n return [func(*args, **kwargs)\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py\", line 288, in \n return [func(*args, **kwargs)\n File \"/tmp/ipykernel_600570/1202779090.py\", line 117, in resample_procced_to_realfslr32\n File \"/tmp/ipykernel_600570/1202779090.py\", line 89, in create_fslr32k_sample\n File \"/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/subprocess.py\", line 528, in run\n raise CalledProcessError(retcode, process.args,\nsubprocess.CalledProcessError: Command '['wb_command', '-cifti-create-dense-timeseries', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii', '-volume', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz', '/data/MLDSST/nielsond/target_test/other_repos/HCPpipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz', '-left-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/lh.32k_fs_LR.shape.gii', '-roi-left', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.L.atlasroi.32k_fs_LR.shape.gii', '-right-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/rh.32k_fs_LR.shape.gii', '-roi-right', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.R.atlasroi.32k_fs_LR.shape.gii', '-timestep', '2.5']' returned non-zero exit status 255.\n\"\"\"", "\nThe above exception was the direct cause of the following exception:\n", - "\u001B[0;31mCalledProcessError\u001B[0m Traceback (most recent call last)", - "Cell \u001B[0;32mIn[78], line 1\u001B[0m\n\u001B[0;32m----> 1\u001B[0m res \u001B[38;5;241m=\u001B[39m \u001B[43mParallel\u001B[49m\u001B[43m(\u001B[49m\u001B[43mn_jobs\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;241;43m14\u001B[39;49m\u001B[43m,\u001B[49m\u001B[43m \u001B[49m\u001B[43mverbose\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;241;43m10\u001B[39;49m\u001B[43m)\u001B[49m\u001B[43m(\u001B[49m\u001B[43mjobs\u001B[49m\u001B[43m)\u001B[49m\n", - "File \u001B[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py:1098\u001B[0m, in \u001B[0;36mParallel.__call__\u001B[0;34m(self, iterable)\u001B[0m\n\u001B[1;32m 1095\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_iterating \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;01mFalse\u001B[39;00m\n\u001B[1;32m 1097\u001B[0m \u001B[38;5;28;01mwith\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_backend\u001B[38;5;241m.\u001B[39mretrieval_context():\n\u001B[0;32m-> 1098\u001B[0m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mretrieve\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 1099\u001B[0m \u001B[38;5;66;03m# Make sure that we get a last message telling us we are done\u001B[39;00m\n\u001B[1;32m 1100\u001B[0m elapsed_time \u001B[38;5;241m=\u001B[39m time\u001B[38;5;241m.\u001B[39mtime() \u001B[38;5;241m-\u001B[39m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_start_time\n", - "File \u001B[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py:975\u001B[0m, in \u001B[0;36mParallel.retrieve\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 973\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[1;32m 974\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mgetattr\u001B[39m(\u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_backend, \u001B[38;5;124m'\u001B[39m\u001B[38;5;124msupports_timeout\u001B[39m\u001B[38;5;124m'\u001B[39m, \u001B[38;5;28;01mFalse\u001B[39;00m):\n\u001B[0;32m--> 975\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_output\u001B[38;5;241m.\u001B[39mextend(\u001B[43mjob\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mget\u001B[49m\u001B[43m(\u001B[49m\u001B[43mtimeout\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mtimeout\u001B[49m\u001B[43m)\u001B[49m)\n\u001B[1;32m 976\u001B[0m \u001B[38;5;28;01melse\u001B[39;00m:\n\u001B[1;32m 977\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_output\u001B[38;5;241m.\u001B[39mextend(job\u001B[38;5;241m.\u001B[39mget())\n", - "File \u001B[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/_parallel_backends.py:567\u001B[0m, in \u001B[0;36mLokyBackend.wrap_future_result\u001B[0;34m(future, timeout)\u001B[0m\n\u001B[1;32m 564\u001B[0m \u001B[38;5;250m\u001B[39m\u001B[38;5;124;03m\"\"\"Wrapper for Future.result to implement the same behaviour as\u001B[39;00m\n\u001B[1;32m 565\u001B[0m \u001B[38;5;124;03mAsyncResults.get from multiprocessing.\"\"\"\u001B[39;00m\n\u001B[1;32m 566\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 567\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[43mfuture\u001B[49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43mresult\u001B[49m\u001B[43m(\u001B[49m\u001B[43mtimeout\u001B[49m\u001B[38;5;241;43m=\u001B[39;49m\u001B[43mtimeout\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 568\u001B[0m \u001B[38;5;28;01mexcept\u001B[39;00m CfTimeoutError \u001B[38;5;28;01mas\u001B[39;00m e:\n\u001B[1;32m 569\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;167;01mTimeoutError\u001B[39;00m \u001B[38;5;28;01mfrom\u001B[39;00m \u001B[38;5;21;01me\u001B[39;00m\n", - "File \u001B[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/concurrent/futures/_base.py:439\u001B[0m, in \u001B[0;36mFuture.result\u001B[0;34m(self, timeout)\u001B[0m\n\u001B[1;32m 437\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m CancelledError()\n\u001B[1;32m 438\u001B[0m \u001B[38;5;28;01melif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_state \u001B[38;5;241m==\u001B[39m FINISHED:\n\u001B[0;32m--> 439\u001B[0m \u001B[38;5;28;01mreturn\u001B[39;00m \u001B[38;5;28;43mself\u001B[39;49m\u001B[38;5;241;43m.\u001B[39;49m\u001B[43m__get_result\u001B[49m\u001B[43m(\u001B[49m\u001B[43m)\u001B[49m\n\u001B[1;32m 441\u001B[0m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_condition\u001B[38;5;241m.\u001B[39mwait(timeout)\n\u001B[1;32m 443\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_state \u001B[38;5;129;01min\u001B[39;00m [CANCELLED, CANCELLED_AND_NOTIFIED]:\n", - "File \u001B[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/concurrent/futures/_base.py:391\u001B[0m, in \u001B[0;36mFuture.__get_result\u001B[0;34m(self)\u001B[0m\n\u001B[1;32m 389\u001B[0m \u001B[38;5;28;01mif\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_exception:\n\u001B[1;32m 390\u001B[0m \u001B[38;5;28;01mtry\u001B[39;00m:\n\u001B[0;32m--> 391\u001B[0m \u001B[38;5;28;01mraise\u001B[39;00m \u001B[38;5;28mself\u001B[39m\u001B[38;5;241m.\u001B[39m_exception\n\u001B[1;32m 392\u001B[0m \u001B[38;5;28;01mfinally\u001B[39;00m:\n\u001B[1;32m 393\u001B[0m \u001B[38;5;66;03m# Break a reference cycle with the exception in self._exception\u001B[39;00m\n\u001B[1;32m 394\u001B[0m \u001B[38;5;28mself\u001B[39m \u001B[38;5;241m=\u001B[39m \u001B[38;5;28;01mNone\u001B[39;00m\n", - "\u001B[0;31mCalledProcessError\u001B[0m: Command '['wb_command', '-cifti-create-dense-timeseries', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii', '-volume', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz', '/data/MLDSST/nielsond/target_test/other_repos/HCPpipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz', '-left-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/lh.32k_fs_LR.shape.gii', '-roi-left', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.L.atlasroi.32k_fs_LR.shape.gii', '-right-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/rh.32k_fs_LR.shape.gii', '-roi-right', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.R.atlasroi.32k_fs_LR.shape.gii', '-timestep', '2.5']' returned non-zero exit status 255." + "\u001b[0;31mCalledProcessError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[78], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m res \u001b[38;5;241m=\u001b[39m \u001b[43mParallel\u001b[49m\u001b[43m(\u001b[49m\u001b[43mn_jobs\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m14\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mverbose\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m10\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m(\u001b[49m\u001b[43mjobs\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py:1098\u001b[0m, in \u001b[0;36mParallel.__call__\u001b[0;34m(self, iterable)\u001b[0m\n\u001b[1;32m 1095\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_iterating \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m 1097\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_backend\u001b[38;5;241m.\u001b[39mretrieval_context():\n\u001b[0;32m-> 1098\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mretrieve\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1099\u001b[0m \u001b[38;5;66;03m# Make sure that we get a last message telling us we are done\u001b[39;00m\n\u001b[1;32m 1100\u001b[0m elapsed_time \u001b[38;5;241m=\u001b[39m time\u001b[38;5;241m.\u001b[39mtime() \u001b[38;5;241m-\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_start_time\n", + "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/parallel.py:975\u001b[0m, in \u001b[0;36mParallel.retrieve\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 973\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 974\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_backend, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msupports_timeout\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m):\n\u001b[0;32m--> 975\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_output\u001b[38;5;241m.\u001b[39mextend(\u001b[43mjob\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m)\n\u001b[1;32m 976\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 977\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_output\u001b[38;5;241m.\u001b[39mextend(job\u001b[38;5;241m.\u001b[39mget())\n", + "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/site-packages/joblib/_parallel_backends.py:567\u001b[0m, in \u001b[0;36mLokyBackend.wrap_future_result\u001b[0;34m(future, timeout)\u001b[0m\n\u001b[1;32m 564\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Wrapper for Future.result to implement the same behaviour as\u001b[39;00m\n\u001b[1;32m 565\u001b[0m \u001b[38;5;124;03mAsyncResults.get from multiprocessing.\"\"\"\u001b[39;00m\n\u001b[1;32m 566\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 567\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfuture\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mresult\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 568\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m CfTimeoutError \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 569\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mTimeoutError\u001b[39;00m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01me\u001b[39;00m\n", + "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/concurrent/futures/_base.py:439\u001b[0m, in \u001b[0;36mFuture.result\u001b[0;34m(self, timeout)\u001b[0m\n\u001b[1;32m 437\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m CancelledError()\n\u001b[1;32m 438\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_state \u001b[38;5;241m==\u001b[39m FINISHED:\n\u001b[0;32m--> 439\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__get_result\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 441\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_condition\u001b[38;5;241m.\u001b[39mwait(timeout)\n\u001b[1;32m 443\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_state \u001b[38;5;129;01min\u001b[39;00m [CANCELLED, CANCELLED_AND_NOTIFIED]:\n", + "File \u001b[0;32m/gpfs/gsfs10/users/MLDSST/nielsond/target_test/env/lib/python3.9/concurrent/futures/_base.py:391\u001b[0m, in \u001b[0;36mFuture.__get_result\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 389\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception:\n\u001b[1;32m 390\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 391\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_exception\n\u001b[1;32m 392\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 393\u001b[0m \u001b[38;5;66;03m# Break a reference cycle with the exception in self._exception\u001b[39;00m\n\u001b[1;32m 394\u001b[0m \u001b[38;5;28mself\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n", + "\u001b[0;31mCalledProcessError\u001b[0m: Command '['wb_command', '-cifti-create-dense-timeseries', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_fsLR32k.dtseries.nii', '-volume', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/Rest_OCME+MEICA+MGTR_nonlin.nii.gz', '/data/MLDSST/nielsond/target_test/other_repos/HCPpipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz', '-left-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/lh.32k_fs_LR.shape.gii', '-roi-left', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.L.atlasroi.32k_fs_LR.shape.gii', '-right-metric', '/data/EDB/TMSpilot/liston/sub-24740/func/rest/session_1/run_1/rh.32k_fs_LR.shape.gii', '-roi-right', '/data/EDB/TMSpilot/liston/sub-24740/anat/MNINonLinear/fsaverage_LR32k/sub-24740.R.atlasroi.32k_fs_LR.shape.gii', '-timestep', '2.5']' returned non-zero exit status 255." ] } ],