Summary of what happened:
In the QSIRecon documentation, I saw that if using a custom atlas, you need to specify --atlases and --datasets , but I received an error saying atlas_configs was not found.
Besides, the MNI152NLin2009cAsym documentation mentioned report 404 not found. I can’t transform my atlas space. Is the transformation space step not nessecery anymore?
Command used (and if a helper script was used, a link to the helper script or the command generated):
#!/bin/bash
# ... some code unrelated to qsirecon
sub=$FILE
fs_license=/opt/software/freesurfer/license.txt
input_dir=/data/disk0/zhangyi/LGStroke/prep/Left/prep_result/$sub/qsiprep
output_dir=/data/disk0/zhangyi/LGStroke/prep/Left/prep_result/$sub/qsirecon
work_dir=/data/disk0/zhangyi/LGStroke/prep/Left/prep_result/$sub/qsirecon_work
cores=8
pipeline=mrtrix_singleshell_ss3t_ACT-hsvs
atlas_dir=/data/disk0/zhangyi/LGStroke/prep/Left/prep_result/atlases
atlas=Schaefer400Yeo2011networks17
fs_dir=/data/disk0/zhangyi/LGStroke/prep/Left/prep_result/$sub/freesurfer
mkdir -p $work_dir
mkdir -p $output_dir
docker run \
--rm \
--user $(id -u):$(id -g) \
-v $fs_license:/opt/freesurfer/license.txt:ro \
-v $input_dir:/input:ro \
-v $output_dir:/output \
-v $atlas_dir:/atlases \
-v $work_dir:/work \
-v $fs_dir:/fs_dir:ro \
gong.wg:5000/qsirecon:latest \
/input \
/output \
participant \
--work-dir /work \
--nthreads $cores \
--omp-nthreads $cores \
--recon-spec $pipeline \
--datasets /atlases \
--atlases $atlas \
--fs-subjects-dir /fs_dir \
--participant-label $sub
Version:
pennlinc/qsirecon:1.0.0
Relevant log outputs (up to 20 lines):
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 720, in _run_command
result = self._interface.run(cwd=outdir, ignore_exception=True)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 392, in run
self._check_mandatory_inputs()
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 277, in _check_mandatory_inputs
raise ValueError(msg)
ValueError: MRTrixAtlasGraph requires a value for input 'atlas_configs'. For a list of required inputs, see MRTrixAtlasGraph.help()
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/concurrent/futures/process.py", line 246, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result["result"] = node.result
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 221, in result
return _load_resultfile(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/pipeline/engine/utils.py", line 290, in load_resultfile
raise FileNotFoundError(results_file)
FileNotFoundError: /work/qsirecon_1_0_wf/sub-L0011_mrtrix_singleshell_ss3_hsvst/sub_L0011_ses_1_space_T1w_desc_preproc_recon_wf/mrtrix_conn/calc_connectivity/result_calc_connectivity.pklz
Screenshots / relevant information:
zhangyi@node4:/data/disk0/zhangyi/LGStroke/prep/Left/prep_result$ tree -L 2 atlases
atlases/
├── atlas-Schaefer400Yeo2011networks17
│ ├── atlas-Schaefer400Yeo2011networks17_res-1_space-FSLMNI152.nii.gz
│ └── atlas-Schaefer400Yeo2011networks17_res-1_space-FSLMNI152.tsv
└── dataset_description.json
Sincere thanks