Hello 
I am trying to run xcp_d on a high performance computer that does not have access to internet.
I have specified in the script network none, yet it is still trying to access the internet to obtain some atlases (I suspect).
I have uploaded atlases generated when running xcp_d via Docker that is saved in derivatives/sourcedata/atlases. But I believe that the xcptmp working directory requires its own set of atlases. I have seen that for each participant it tries to run that it generates these atlases per participant working directory, so I am not too sure where to save atlases like: tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz
Would I just download the atlases from the AtlasPack available on GitHub and store them in derivatives/sourcedata/atlases?
Command used:
#!/bin/bash
#PBS -P vn67
#PBS -q normal
#PBS -l ncpus=8
#PBS -l mem=16GB
#PBS -l walltime=08:00:00
#PBS -l wd
#PBS -m abe
#PBS -l storage=scratch/vn67+gdata/vn67
module load singularity
IMG=/g/data/vn67/et0688/xcp_d-26.0.2.simg
FMRIPREP=/scratch/vn67/et0688/MPATHY_MRI/MPATHY/fmriprep/prep_derivatives
OUT=/scratch/vn67/et0688/MPATHY_MRI/MPATHY/xcp_d/derivatives
WORK=/scratch/vn67/et0688/MPATHY_MRI/MPATHY/xcptmp/work
mkdir -p ${WORK}
# Extract subject ID from job name
SUBJECT=$PBS_JOBNAME
#echo "Running fmriprep for subject: ${subject}"
echo "Running XCP-D for subject ${SUBJECT}"
singularity exec --cleanenv --network none \
-B ${FMRIPREP}:/fmriprep:ro \
-B ${OUT}:/out:rw \
-B ${WORK}:/work:rw \
-B /scratch/vn67/et0688/MPATHY_MRI/MPATHY/xcp_d/prep_derivatives/freesurfer:/freesurfer:ro \
-B /scratch/vn67/et0688/MPATHY_MRI/MPATHY/fmriprep/Ref_Files/freesurfer.txt:/license.txt:ro \
${IMG} \
xcp_d /fmriprep /out participant \
-w /work \
--participant-label ${SUBJECT} \
--mode none \
--task-id restingstate \
--input-type fmriprep \
--file-format nifti \
--despike \
--head-radius 50 \
--smoothing 6 \
-f 0.3 \
--nuisance-regressors 36P \
--motion-filter-type none \
--output-type censored \
--warp-surfaces-native2std n \
--min-coverage 0.5 \
--fs-license-file /license.txt \
--abcc-qc n \
--linc-qc n \
--combine-runs n \
--create-matrices all \
--output-run-wise-correlations n
Version:
xcp_d-26.0.2
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS
Relevant log outputs (up to 20 lines):
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/app/.pixi/envs/xcp-d/lib/python3.12/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/app/.pixi/envs/xcp-d/lib/python3.12/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/xcp_d/cli/workflow.py", line 94, in build_workflow
retval['workflow'] = init_xcpd_wf()
^^^^^^^^^^^^^^
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/xcp_d/workflows/base.py", line 81, in init_xcpd_wf
single_subject_wf = init_single_subject_wf(subject_id, anat_session, func_sessions)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/xcp_d/workflows/base.py", line 579, in init_single_subject_wf
postprocess_bold_wf = init_postprocess_bold_wf(
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/xcp_d/workflows/bold/nifti.py", line 325, in init_postprocess_nifti_wf
qc_report_wf = init_qc_report_wf(
^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/xcp_d/workflows/bold/plotting.py", line 236, in init_qc_report_wf
get_template(
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/templateflow/client.py", line 249, in get
_s3_get(self.cache.config, filepath)
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/templateflow/client.py", line 387, in _s3_get
r = requests.get(url, stream=True, timeout=config.timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, **send_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/requests/adapters.py", line 677, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='templateflow.s3.amazonaws.com', port=443): Max retries exceeded with url: /tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz (Caused by NewConnectionError("HTTPSConnection(host='templateflow.s3.amazonaws.com', port=443): Failed to establish a new connection: [Errno 101] Network is unreachable"))
Thank you!!