Hello all,
I am trying to complete the BIDS/fMRIPrep tutorial from Andy’s Brain Book and am running into problems in preprocessing.
Here’s the config from the verbose command:
fMRIPrep config:
[environment]
cpu_count = 24
exec_env = "singularity"
free_mem = 190.5
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.6.1"
templateflow_version = "0.7.2"
version = "21.0.4"
[execution]
bids_dir = "/home/vagrant/DATA/BIDS_tutorial"
bids_database_dir = "/home/vagrant/DATA/work/20221127-005903_c7f81f20-7f31-4640-9b66-1e2f2129f41f/bids_db"
bids_description_hash = "642036db1ea7da4f7ce4c915f6c75e81cc5535d7d4bde327cb228d982ffff16b"
boilerplate_only = false
sloppy = false
debug = []
fmriprep_dir = "/home/vagrant/DATA/BIDS_tutorial/derivatives"
fs_license_file = "/home/vagrant/DATA/Resources/license.txt"
fs_subjects_dir = "/home/vagrant/DATA/BIDS_tutorial/derivatives/sourcedata/freesurfer"
layout = "BIDS Layout: ...ome/vagrant/DATA/BIDS_tutorial | Subjects: 1 | Sessions: 1 | Runs: 2"
log_dir = "/home/vagrant/DATA/BIDS_tutorial/derivatives/logs"
log_level = 15
low_mem = true
md_only_boilerplate = true
notrack = false
output_dir = "/home/vagrant/DATA/BIDS_tutorial/derivatives"
me_output_echos = false
output_layout = "bids"
output_spaces = "MNI152NLin2009cAsym:res-2"
reports_only = false
run_uuid = "20221127-005903_c7f81f20-7f31-4640-9b66-1e2f2129f41f"
participant_label = [ "01",]
templateflow_home = "/home/vagrant/DATA/Resources/templateflow"
work_dir = "/home/vagrant/DATA/work"
write_graph = false
[workflow]
anat_only = false
aroma_err_on_warn = false
aroma_melodic_dim = -200
bold2t1w_dof = 6
bold2t1w_init = "register"
cifti_output = false
fmap_bspline = false
force_syn = false
hires = true
ignore = []
longitudinal = false
medial_surface_nan = false
regressors_all_comps = false
regressors_dvars_th = 1.5
regressors_fd_th = 0.5
run_reconall = false
skull_strip_fixed_seed = false
skull_strip_template = "OASIS30ANTs"
skull_strip_t1w = "force"
slice_time_ref = 0.5
spaces = "MNI152NLin2009cAsym:res-2"
topup_max_vols = 5
use_aroma = false
use_syn_sdc = false
[nipype]
crashfile_format = "txt"
get_linked_libs = false
memory_gb = 195.0
nprocs = 16
omp_nthreads = 8
plugin = "MultiProc"
resource_monitor = false
stop_on_first_crash = true
[seeds]
master = 55317
ants = 40395
numpy = 18737
[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false
It works fine until it attempts to start node fsl2itk. Here are the warning and error messages:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_bart_run_01_wf.initial_boldref_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
221128-02:47:49,857 nipype.workflow WARNING:
Storing result file without outputs
221128-02:47:49,875 nipype.workflow WARNING:
[Node] Error on "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_bart_run_01_wf.bold_hmc_wf.fsl2itk" (/home/vagrant/DATA/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_bart_run_01_wf/bold_hmc_wf/fsl2itk)
221128-02:47:49,895 nipype.workflow ERROR:
Node fsl2itk failed to run on host vagrant.
221128-02:47:49,924 nipype.workflow ERROR:
Saving crash info to /home/vagrant/DATA/BIDS_tutorial/derivatives/sub-01/log/20221128-023819_0e821647-f1ec-476a-a7d1-1bb91f9ea8a8/crash-20221128-024749-root-fsl2itk-0d871f02-4eba-4f5e-bc90-83d568d2cdff.txt
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/itk.py", line 94, in _run_interface
itk_outs = [
File "/opt/conda/lib/python3.8/tempfile.py", line 827, in __exit__
self.cleanup()
File "/opt/conda/lib/python3.8/tempfile.py", line 831, in cleanup
self._rmtree(self.name)
File "/opt/conda/lib/python3.8/tempfile.py", line 813, in _rmtree
_shutil.rmtree(name, onerror=onerror)
File "/opt/conda/lib/python3.8/shutil.py", line 722, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File "/opt/conda/lib/python3.8/shutil.py", line 720, in rmtree
os.rmdir(path)
OSError: [Errno 26] Text file busy: '/home/vagrant/DATA/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_bart_run_01_wf/bold_hmc_wf/fsl2itk/tmp-otsvqilg'
221128-02:47:50,44 nipype.workflow CRITICAL:
fMRIPrep failed: Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/itk.py", line 94, in _run_interface
itk_outs = [
File "/opt/conda/lib/python3.8/tempfile.py", line 827, in __exit__
self.cleanup()
File "/opt/conda/lib/python3.8/tempfile.py", line 831, in cleanup
self._rmtree(self.name)
File "/opt/conda/lib/python3.8/tempfile.py", line 813, in _rmtree
_shutil.rmtree(name, onerror=onerror)
File "/opt/conda/lib/python3.8/shutil.py", line 722, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File "/opt/conda/lib/python3.8/shutil.py", line 720, in rmtree
os.rmdir(path)
OSError: [Errno 26] Text file busy: '/home/vagrant/DATA/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_bart_run_01_wf/bold_hmc_wf/fsl2itk/tmp-otsvqilg'
221128-02:47:53,723 cli ERROR:
Preprocessing did not finish successfully. Errors occurred while processing data from participants: 01 (1). Check the HTML reports for details.
I have not been able to find any help online and would appreciate any insight!