C-PAC v1.8.1-dev @ 53ab684 ― brainlife

[shnizzedy]

Description

https://github.com/FCP-INDI/C-PAC/pull/1531 on Brainlife

Version

v1.8.1-dev @ https://github.com/FCP-INDI/C-PAC/commit/53ab684fd21ddc2644b55d3a0c06a2d31db97f24

Container

fix_multiple_custom_regressors

System

brainlife

Data Size

No response

Results

https://brainlife.io/project/5f299e1fbeafe973f362a972/process/6140e1e48fcfda264a6c433f

crash-20210914-232319-user-21_md_7_2-d7455dd1-2e6e-47e2-a41f-dabd7402bc87.txt:

Node: cpac_sub-A00025566_ses-DS2.anat_skullstrip_ants.atropos_wf.21_md_7_2
Working directory: /output/working/cpac_sub-A00025566_ses-DS2/anat_skullstrip_ants/atropos_wf/21_md_7_2

Node inputs:

args = <undefined>
dimension = 3
environ = {'NSLOTS': '1'}
num_threads = 1
op1 = /output/working/cpac_sub-A00025566_ses-DS2/anat_skullstrip_ants/atropos_wf/20_add_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz
op2 = 5
operation = MD
output_image = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 566, in move
    os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: '/output/working/cpac_sub-A00025566_ses-DS2/anat_skullstrip_ants/atropos_wf/21_md_7_2/_0x1b770e1ff602706f59f442785ca7431b_unfinished.json' -> '/output/working/cpac_sub-A00025566_ses-DS2/anat_skullstrip_ants/atropos_wf/21_md_7_2/_0x1b770e1ff602706f59f442785ca7431b.json'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py", line 46, in run
    node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 531, in run
    shutil.move(hashfile_unfinished, hashfile_unfinished.replace("_unfinished", ""))
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 580, in move
    copy_function(src, real_dst)
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 266, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/usr/local/miniconda/lib/python3.7/shutil.py", line 120, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: '/output/working/cpac_sub-A00025566_ses-DS2/anat_skullstrip_ants/atropos_wf/21_md_7_2/_0x1b770e1ff602706f59f442785ca7431b_unfinished.json'

Run Command:

main:

#!/bin/bash
#PBS -l nodes=1:ppn=8,walltime=48:00:00
#PBS -l vmem=30gb
#PBS -N cpac

# parse config.json for input parameters
preconfig=$(jq -r .preconfig config.json)
if [ "$preconfig" == "" ] || [ "$preconfig" == "null" ] || [ "$preconfig" == "default" ]
    then
        preconfig=""
    else
        preconfig="--preconfig $preconfig"
fi

# get latest image if we don't already have one
if [ -f cpac-singularity-image.simg ]
  then
    echo "using existing C-PAC Singularity image"
  else
    echo "getting C-PAC Singularity image"
    time curl -LOJ https://9514-4733263-gh.circle-artifacts.com/0/cpac-singularity-image.simg
fi

# convert brainlife structure to BIDS
if [ ! -d bids ]
  then
    echo "restructuring data"
    bl2bids
fi

set -x
set -e

# run C-PAC
echo "running C-PAC"
mkdir -p output tmp

time singularity run -e -B $PWD/bids:/bids -B $PWD/output:/output -B $PWD/tmp:/tmp cpac-singularity-image.simg /bids /output participant $preconfig --save_working_dir

with config.json:

{
    "t1": "../6140e1e58fcfdad61d6c4349/59a5f2a1c1e7111a78d11a64/t1.nii.gz",
    "bold": "../6140e1e58fcfdad61d6c4349/59cc5342f45e7344b8c8b020/bold.nii.gz",
    "events": "../6140e1e58fcfdad61d6c4349/59cc5342f45e7344b8c8b020/events.tsv",
    "events_json": "../6140e1e58fcfdad61d6c4349/59cc5342f45e7344b8c8b020/events.json",
    "sbref": "../6140e1e58fcfdad61d6c4349/59cc5342f45e7344b8c8b020/sbref.nii.gz",
    "sbref_json": "../6140e1e58fcfdad61d6c4349/59cc5342f45e7344b8c8b020/sbref.json",
    "physio": "../6140e1e58fcfdad61d6c4349/59cc5342f45e7344b8c8b020/physio.tsv.gz",
    "physio_json": "../6140e1e58fcfdad61d6c4349/59cc5342f45e7344b8c8b020/physio.json",
    "preconfig": "fmriprep-options",
    "_app": "5f3593e84615e04651bf9364",
    "_tid": 2,
    "_inputs": [
        {
            "id": "t1",
            "datatype": "58c33bcee13a50849b25879a",
            "meta": {
                "subject": "A00025566",
                "session": "DS2"
            },
            "tags": [
                "DS2"
            ],
            "datatype_tags": [],
            "subdir": "59a5f2a1c1e7111a78d11a64",
            "dataset_id": "59a5f2a1c1e7111a78d11a64",
            "project": "59a57af4b5e93a0023001416",
            "task_id": "6140e1e58fcfdad61d6c4349",
            "keys": [
                "t1"
            ]
        },
        {
            "id": "func",
            "datatype": "59b685a08e5d38b0b331ddc5",
            "meta": {
                "subject": "A00025566",
                "session": "DS2",
                "task": "rest",
                "acquisition": "645"
            },
            "tags": [
                "DS2",
                "rest",
                "645"
            ],
            "datatype_tags": [
                "rest"
            ],
            "subdir": "59cc5342f45e7344b8c8b020",
            "dataset_id": "59cc5342f45e7344b8c8b020",
            "project": "59a57af4b5e93a0023001416",
            "task_id": "6140e1e58fcfdad61d6c4349",
            "keys": [
                "bold",
                "events",
                "events_json",
                "sbref",
                "sbref_json",
                "physio",
                "physio_json"
            ]
        }
    ],
    "_outputs": [
        {
            "id": "output",
            "datatype": "59c3eae633fc1cf9ead71679",
            "desc": "C-PAC",
            "meta": {
                "subject": "A00025566",
                "session": "DS2"
            },
            "subdir": "output",
            "datatype_tags": [
                "c-pac"
            ]
        }
    ]
}

Pipeline Config

cpac_pipeline_config_2021-09-14T20-01-06Z.yml

Data Config

cpac_data_config_2021-09-14T20-01-06Z.yml.txt

Default Pipeline Diff

cpac_pipeline_config_2021-09-14T20-01-06Z_min.yml

Screenshots of brain extraction and registration wireframe overlays from QC pages

No response

Node timing information

No response

Extracted time series 1D and nuisance regressors 1D correlations against previous version or some benchmark

No response

[shnizzedy]

This run is a re-run of #21 with a different subject