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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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'DynamicTraitedSpec' object has no attribute 'T1w_preproc' #3160

Closed juansanchezpena closed 10 months ago

juansanchezpena commented 10 months ago

What happened?

fMRIPrep failed: 'DynamicTraitedSpec' object has no attribute 'T1w_preproc' Ran using docker on three test cases and all failed with same error

What command did you use?

admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:25,447 nipype.workflow IMPORTANT:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Running fMRIPrep version 23.2.0a1
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |         29 Files, 2.3GB        resting                 MRI
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |         1 - Subject            gbu
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          License NOTICE ##################################################
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |         1 - Session
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          fMRIPrep 23.2.0a1
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |
docker service create --constraint 'node.hostname==plisskenmri.nyspi.local' --replicas 1 --reserve-cpu 8 --reserve-memory 32g --mode replicated --restart-condition none --mount type=bind,source=$indir,destination=/input,readonly=true --mount type=bind,source=$outdir,destination=/output  --mount type=bind,source=/MRI_DATA/bin/freesurferlicense.txt,destination=/opt/freesurfer/license.txt,readonly=true   nipreps/fmriprep:23.2.0a1  /input /output  participant $addarg

subfmri-arg-23.2.0a1 -i /MRI_DATA/mritesting/patensasc/rawdata -o /MRI_DATA/mritesting/patensasc/derivatives/subfmri-arg-23.2.0a1 -l /MRI_DATA/mritesting/patensasc/derivatives/subfmri-arg-23.2.0a1/patensasc0085.log -a "--participant-label patensasc0085 --output-spaces T1w MNI152NLin2009cAsym:res-2 --cifti-output  --project-goodvoxels”

What version of fMRIPrep are you running?

23.2.0a1

How are you running fMRIPrep?

Docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

sanchezj@mrimaker:/MRI_DATA/mritesting/patensasc/derivatives/subfmri-arg-23.2.0a1/sub-patensasc0085/log/20231128-142805_4b6ecc4d-9578-41da-9fc2-666f67258b4d$ cat fmriprep.toml 
[environment]
cpu_count = 24
exec_env = "docker"
free_mem = 116.2
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.8.6"
templateflow_version = "23.1.0"
version = "23.2.0a1"

[execution]
bids_dir = "/input"
derivatives = []
bids_database_dir = "/tmp/work/20231128-142805_4b6ecc4d-9578-41da-9fc2-666f67258b4d/bids_db"
bids_description_hash = "6ef18c859337aa2808b2b7a6da1c25dea0724d5fcbbf2a2b56a23b07ae39f803"
boilerplate_only = false
sloppy = false
debug = []
fmriprep_dir = "/output"
fs_license_file = "/opt/freesurfer/license.txt"
fs_subjects_dir = "/output/sourcedata/freesurfer"
layout = "BIDS Layout: .../input | Subjects: 1 | Sessions: 1 | Runs: 4"
log_dir = "/output/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
notrack = false
track_carbon = false
country_code = "CAN"
output_dir = "/output"
me_output_echos = false
output_layout = "bids"
output_spaces = "T1w MNI152NLin2009cAsym:res-2"
reports_only = false
run_uuid = "20231128-142805_4b6ecc4d-9578-41da-9fc2-666f67258b4d"
participant_label = [ "patensasc0085",]
templateflow_home = "/home/fmriprep/.cache/templateflow"
work_dir = "/tmp/work"
write_graph = false

[workflow]
anat_only = false
aroma_err_on_warn = false
aroma_melodic_dim = 0
bold2t1w_dof = 6
bold2t1w_init = "register"
cifti_output = "91k"
fmap_bspline = false
force_syn = false
hires = true
ignore = []
level = "full"
longitudinal = false
run_msmsulc = true
medial_surface_nan = false
project_goodvoxels = true
regressors_all_comps = false
regressors_dvars_th = 1.5
regressors_fd_th = 0.5
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "OASIS30ANTs"
skull_strip_t1w = "force"
slice_time_ref = 0.5
spaces = "T1w MNI152NLin2009cAsym:res-2 MNI152NLin6Asym:res-2"
use_aroma = false
use_syn_sdc = false
me_t2s_fit_method = "curvefit"

[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 24
omp_nthreads = 8
plugin = "MultiProc"
remove_unnecessary_outputs = true
resource_monitor = false
stop_on_first_crash = false

[seeds]
master = 47673
ants = 19166
numpy = 47016

[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false

nmri.nyspi.local    | bids-validator@1.13.1
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | bids-validator@1.13.1
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | (node:10) Warning: Closing directory handle on garbage collection
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | (Use `node --trace-warnings ...` to show where the warning was created)
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |     1: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible. (code: 113 - NO_AUTHORS)
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |     1: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered because there are no authors, which will make DOI registration from dataset metadata impossible. (code: 113 - NO_AUTHORS)
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |     Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |     Please visit https://neurostars.org/search?q=NO_AUTHORS for existing conversations about this issue.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |     2: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |     2: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |         ./README
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |         ./README
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |     Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |     Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |         Summary:               Available Tasks:        Available Modalities: 
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |         29 Files, 2.3GB        gbu                     MRI                   
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |         Summary:               Available Tasks:        Available Modalities: 
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |         29 Files, 2.3GB        resting                 MRI                   
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |         1 - Subject            resting                                       
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |         1 - Subject            gbu                                           
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |         1 - Session                                                          
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |         1 - Session                                                          
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |     If you have any questions, please post on https://neurostars.org/tags/bids.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | (node:9) Warning: Closing directory handle on garbage collection
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | (Use `node --trace-warnings ...` to show where the warning was created)
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:25,447 nipype.workflow IMPORTANT:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Running fMRIPrep version 23.2.0a1
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |     If you have any questions, please post on https://neurostars.org/tags/bids.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          License NOTICE ##################################################
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          fMRIPrep 23.2.0a1
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          Copyright 2023 The NiPreps Developers.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:33,960 nipype.workflow IMPORTANT:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          This product includes software developed by
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Running fMRIPrep version 23.2.0a1
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          the NiPreps Community (https://nipreps.org/).
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          Portions of this software were developed at the Department of
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          License NOTICE ##################################################
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          Psychology at Stanford University, Stanford, CA, US.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          fMRIPrep 23.2.0a1
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          This software is also distributed as a Docker container image.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          The bootstrapping file for the image ("Dockerfile") is licensed
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          under the MIT License.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          Copyright 2023 The NiPreps Developers.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          This software may be distributed through an add-on package called
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          This product includes software developed by
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          "Docker Wrapper" that is under the BSD 3-clause License.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |          #################################################################
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          the NiPreps Community (https://nipreps.org/).
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:25,626 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          Portions of this software were developed at the Department of
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          Psychology at Stanford University, Stanford, CA, US.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Building fMRIPrep's workflow:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |            * BIDS dataset path: /input.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          This software is also distributed as a Docker container image.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |            * Participant list: ['patensasc0085'].
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          The bootstrapping file for the image ("Dockerfile") is licensed
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          under the MIT License.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |            * Run identifier: 20231128-142805_4b6ecc4d-9578-41da-9fc2-666f67258b4d.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          This software may be distributed through an add-on package called
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |            * Output spaces: T1w MNI152NLin2009cAsym:res-2.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          "Docker Wrapper" that is under the BSD 3-clause License.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |            * Pre-run FreeSurfer's SUBJECTS_DIR: /output/sourcedata/freesurfer.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |          #################################################################
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:26,582 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:34,47 nipype.workflow IMPORTANT:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 1: Adding template workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Building fMRIPrep's workflow:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,38 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 2: Preparing brain extraction workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |            * BIDS dataset path: /input.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,216 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 3: Preparing segmentation workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |            * Participant list: ['patensasc0085'].
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |            * Run identifier: 20231127-193115_42e930b1-8563-4b81-a7e8-d456288cf1a7.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,228 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |            * Output spaces: T1w MNI152NLin2009cAsym:res-2.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym', 'MNI152NLin6Asym']
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,252 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |            * Pre-run FreeSurfer's SUBJECTS_DIR: /output/sourcedata/freesurfer.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:34,787 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 5: Preparing surface reconstruction workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,300 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 1: Adding template workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 6: Preparing mask refinement workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,306 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,103 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 7: Creating T2w template
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,325 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 2: Preparing brain extraction workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,246 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,369 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 3: Preparing segmentation workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,256 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym', 'MNI152NLin6Asym']
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,385 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 8a: Creating cortical ribbon mask
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,393 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 9: Creating fsLR registration sphere
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,276 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,401 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      ANAT Stage 10: Creating MSM-Sulc registration sphere
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 5: Preparing surface reconstruction workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,316 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:27,942 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 6: Preparing mask refinement workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      B0 field inhomogeneity map will be estimated with the following 2 estimator(s): [<EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>].
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,321 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:28,565 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 7: Creating T2w template
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Setting-up fieldmap "fMRI_2" (EstimatorType.PEPOLAR) with <sub-patensasc0085_ses-1173_dir-fpe_run-02_epi.nii.gz, sub-patensasc0085_ses-1173_dir-rpe_run-02_epi.nii.gz>
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,337 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:28,810 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Setting-up fieldmap "fMRI_1" (EstimatorType.PEPOLAR) with <sub-patensasc0085_ses-1173_dir-fpe_run-01_epi.nii.gz, sub-patensasc0085_ses-1173_dir-rpe_run-01_epi.nii.gz>
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:29,633 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,378 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:29,650 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,394 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 8a: Creating cortical ribbon mask
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:29,668 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,402 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 9: Creating fsLR registration sphere
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:29,783 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,410 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      ANAT Stage 10: Creating MSM-Sulc registration sphere
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:30,821 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:35,906 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:30,838 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      B0 field inhomogeneity map will be estimated with the following 2 estimator(s): [<EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>].
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:36,427 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:30,851 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Setting-up fieldmap "fMRI_1" (EstimatorType.PEPOLAR) with <sub-patensasc0085_ses-1173_dir-fpe_run-01_epi.nii.gz, sub-patensasc0085_ses-1173_dir-rpe_run-01_epi.nii.gz>
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:36,677 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:30,969 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Setting-up fieldmap "fMRI_2" (EstimatorType.PEPOLAR) with <sub-patensasc0085_ses-1173_dir-fpe_run-02_epi.nii.gz, sub-patensasc0085_ses-1173_dir-rpe_run-02_epi.nii.gz>
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:37,108 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:31,954 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:37,122 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:31,970 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:37,138 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:31,982 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:37,231 nipype.workflow IMPORTANT:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:38,201 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:32,91 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:38,213 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:33,74 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:38,224 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:33,90 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:38,316 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:39,431 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:33,102 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:39,444 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:39,454 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:33,209 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:39,545 nipype.workflow IMPORTANT:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:34,206 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:40,465 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:40,481 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:34,221 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:40,494 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:34,234 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:40,606 nipype.workflow IMPORTANT:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:34,343 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:41,554 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 1: Adding HMC boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:41,567 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 2: Adding motion correction workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:28:41,754 nipype.workflow INFO:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:41,577 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      fMRIPrep workflow graph with 1635 nodes built successfully.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      Stage 3: Adding coregistration boldref workflow
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:29:01,913 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:41,682 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      BOLD series will be slice-timing corrected to an offset of 0.409s.
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      fMRIPrep started!
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:31:48,496 nipype.workflow INFO:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    | 231128-14:29:04,290 nipype.workflow CRITICAL:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      fMRIPrep workflow graph with 1635 nodes built successfully.
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:32:08,158 nipype.workflow IMPORTANT:
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      fMRIPrep started!
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    | 231127-19:32:10,626 nipype.workflow CRITICAL:
admiring_leakey.1.y75uawmasocb@plisskenmri.nyspi.local    |      fMRIPrep failed: 'DynamicTraitedSpec' object has no attribute 'T1w_preproc'
admiring_leakey.1.jyhwspeepyyf@plisskenmri.nyspi.local    |      fMRIPrep failed: 'DynamicTraitedSpec' object has no attribute 'T1w_preproc'

Additional information / screenshots

No response

mgxd commented 10 months ago

This is fixed in 23.2.0a2, please use that release