Hi there,
I was trying to add the “MNI152NLin6Sym” template (among the valid keywords: “MNI152Lin”, “MNI152NLin2009cAsym”, “MNI152NLin6Asym”, “MNI152NLin6Sym”, “MNIInfant”, “MNIPediatricAsym”, “NKI”, “OASIS30ANTs”, “PNC”, “UNCInfant”, “fsLR”, “fsaverage”, “fsaverage5”, “fsaverage6” at the Usage Notes) to the output spaces when I was running fMRIPrep(docker), but it seems something went wrong, as the logs mentioned below.
Could anyone please help me with the ploblem? Thanks!
All the best,
HK Li
fMRIPrep version: 20.2.1
The crash logs:
Node: fmriprep_wf.single_subject_HBNUHA006_wf.func_preproc_ses_1_task_rest_wf.bold_std_trans_wf.select_tpl
Working directory: /tmp/work/fmriprep_wf/single_subject_HBNUHA006_wf/func_preproc_ses_1_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Sym.resnative/select_tpl
Node inputs:
function_str = def _select_template(template):
from niworkflows.utils.misc import get_template_specs
template, specs = template
template = template.split(’:’)[0] # Drop any cohort modifier if present
specs = specs.copy()
specs[‘suffix’] = specs.get(‘suffix’, ‘T1w’)
# Sanitize resolution
res = specs.pop('res', None) or specs.pop('resolution', None) or 'native'
if res != 'native':
specs['resolution'] = res
return get_template_specs(template, template_spec=specs)[0]
# Map nonstandard resolutions to existing resolutions
specs['resolution'] = 2
try:
out = get_template_specs(template, template_spec=specs)
except RuntimeError:
specs['resolution'] = 1
out = get_template_specs(template, template_spec=specs)
return out[0]
template = (‘MNI152NLin6Sym’, {‘res’: ‘native’})
Traceback (most recent call last):
File “”, line 17, in _select_template
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/utils/misc.py”, line 64, in get_template_specs
in_template, template_spec
RuntimeError: Could not find template “MNI152NLin6Sym” with specs={‘suffix’: ‘T1w’, ‘resolution’: 2, ‘desc’: None, ‘atlas’: None}. Please revise your template argument.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/connection.py”, line 171, in _new_conn
(self._dns_host, self.port), self.timeout, **extra_kw)
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/util/connection.py”, line 79, in create_connection
raise err
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/util/connection.py”, line 69, in create_connection
sock.connect(sa)
TimeoutError: [Errno 110] Connection timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 600, in urlopen
chunked=chunked)
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 343, in _make_request
self._validate_conn(conn)
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 849, in _validate_conn
conn.connect()
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/connection.py”, line 314, in connect
conn = self._new_conn()
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/connection.py”, line 180, in _new_conn
self, “Failed to establish a new connection: %s” % e)
urllib3.exceptions.NewConnectionError: <urllib3.connection.VerifiedHTTPSConnection object at 0x7f59e8fcc5f8>: Failed to establish a new connection: [Errno 110] Connection timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/requests/adapters.py”, line 445, in send
timeout=timeout
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/connectionpool.py”, line 638, in urlopen
_stacktrace=sys.exc_info()[2])
File “/usr/local/miniconda/lib/python3.7/site-packages/urllib3/util/retry.py”, line 398, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host=‘templateflow.s3.amazonaws.com’, port=443): Max retries exceeded with url: /tpl-MNI152NLin6Sym/tpl-MNI152NLin6Sym_res-01_T1w.nii.gz (Caused by NewConnectionError(’<urllib3.connection.VerifiedHTTPSConnection object at 0x7f59e8fcc5f8>: Failed to establish a new connection: [Errno 110] Connection timed out’))
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/multiproc.py”, line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 419, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/utility/wrappers.py”, line 142, in _run_interface
out = function_handle(**args)
File “”, line 20, in _select_template
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/utils/misc.py”, line 58, in get_template_specs
tpl_target_path = get_template(in_template, **template_spec)
File “/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py”, line 68, in get
_s3_get(filepath)
File “/usr/local/miniconda/lib/python3.7/site-packages/templateflow/api.py”, line 208, in _s3_get
r = requests.get(url, stream=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/requests/api.py”, line 72, in get
return request(‘get’, url, params=params, **kwargs)
File “/usr/local/miniconda/lib/python3.7/site-packages/requests/api.py”, line 58, in request
return session.request(method=method, url=url, **kwargs)
File “/usr/local/miniconda/lib/python3.7/site-packages/requests/sessions.py”, line 512, in request
resp = self.send(prep, **send_kwargs)
File “/usr/local/miniconda/lib/python3.7/site-packages/requests/sessions.py”, line 622, in send
r = adapter.send(request, **kwargs)
File “/usr/local/miniconda/lib/python3.7/site-packages/requests/adapters.py”, line 513, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host=‘templateflow.s3.amazonaws.com’, port=443): Max retries exceeded with url: /tpl-MNI152NLin6Sym/tpl-MNI152NLin6Sym_res-01_T1w.nii.gz (Caused by NewConnectionError(’<urllib3.connection.VerifiedHTTPSConnection object at 0x7f59e8fcc5f8>: Failed to establish a new connection: [Errno 110] Connection timed out’))