Hello
Thanks to the Poldrack lab for developing such awesome tools! I am seeking to use fitlins on some data preprocessed using fmriprep. I have the following issues/questions:
-
What I am seeking to do is, at the run level, regress out any variability attributable to the motion parameters and framewise displacement. I then want to look at the residuals (for some SNR measurements). Will fitlins automatically output the residuals from the GLMs?
-
Is a high-pass filter applied to the data prior to fitting the GLM? This thread on the fitlins
github repository [https://github.com/poldracklab/fitlins/issues/12] suggests that it is. If it is applied,
is it possible to provide more details re: the filter? If not, what do you recommend when using
fmriprep and fitlins? -
I am having the below problem actually using fitlins. Please could you let me know if there is a bug or if I am missing something? (Apologies if I am getting the error because of something simple I have missed…) All info muchly appreciated!
Below I provide my file structure, singularity command, model file, and the output from -vvv
I have the following file structure, having acquired functional data
Under:
/scratch/xxx/username/
BIDSdata/
sub-01/
ses-01/
etc...
PREPdata/
fmriprep/
sub-01/
etc...
ANALYZED/
TR1510/
work/
models/
`
and I am using the following singularity command:
singularity run --cleanenv \
-B /scratch/xxx/username/BIDSdata:/scratch/xxx/username/BIDSdata \
-B /scratch/xxx/username/PREPdata/fmriprep:/scratch/xxx/username/PREPdata/fmriprep \
-B /scratch/xxx/username/ANALYZED/TR1510:/scratch/xxx/username/ANALYZED/TR1510 \
-B /scratch/xxx/username/work:/scratch/xxx/username/work \
-B /scratch/xxx/username/models:/scratch/xxx/username/models \
my_images/fitlins-0.6.2.simg \
/scratch/xxx/username/BIDSdata /scratch/xxx/username/ANALYZED/TR1510 run \
-d /scratch/xxx/username/PREPdata/fmriprep \
-w /scratch/xxx/username/work \
-m /scratch/xxx/username/models/model-mc_wp1_move_TR_1510_smdl.json \
--space MNI152NLin2009cAsym \
-vvv
and this is the contents of my model json file:
{
"Name": "mc_wp1_move_TR_1510",
"Description": "model to remove variance due to movement for tSNR - TR 1510",
"Input": {
"task": "learnAtt",
"TR": 1510
},
"Steps": [
{
"Level": "run",
"Model": {
"X": [
"framewise_displacement", "trans_x", "trans_x_derivative1", "trans_y", "trans_y_derivative1", "trans_z", "trans_z_derivative1", "rot_x", "rot_x_derivative1", "rot_y", "rot_y_derivative1", "rot_z", "rot_z_derivative1"
]
}
}
]
}
and here is alllllllll the output from running the command/ the -vvv output (I am particularly wondering about the meaning of AttributeError: ‘RunNode’ object has no attribute ‘get_collections’? (see below)
200220-16:24:16,381 nipype.utils INFO:
Running nipype version 1.3.1 (latest: 1.4.2)
200220-16:24:16,387 nipype.workflow DEBUG:
adding multipath trait: bold_file
200220-16:24:16,388 nipype.workflow DEBUG:
adding multipath trait: session_info
200220-16:24:16,389 nipype.workflow DEBUG:
adding multipath trait: bold_file
200220-16:24:16,389 nipype.workflow DEBUG:
adding multipath trait: contrast_info
200220-16:24:16,389 nipype.workflow DEBUG:
adding multipath trait: design_matrix
200220-16:24:16,389 nipype.workflow DEBUG:
adding multipath trait: mask_file
200220-16:24:16,395 nipype.workflow DEBUG:
adding multipath trait: tsv
200220-16:24:16,396 nipype.workflow DEBUG:
adding multipath trait: entities
200220-16:24:16,396 nipype.workflow DEBUG:
adding multipath trait: in_file
200220-16:24:16,397 nipype.workflow DEBUG:
adding multipath trait: data
200220-16:24:16,397 nipype.workflow DEBUG:
adding multipath trait: contrast_info
200220-16:24:16,397 nipype.workflow DEBUG:
adding multipath trait: data
200220-16:24:16,398 nipype.workflow DEBUG:
adding multipath trait: contrast_info
200220-16:24:16,398 nipype.workflow DEBUG:
adding multipath trait: data
200220-16:24:16,399 nipype.workflow DEBUG:
adding multipath trait: entities
200220-16:24:16,399 nipype.workflow DEBUG:
adding multipath trait: in_file
200220-16:24:16,400 nipype.workflow DEBUG:
adding multipath trait: entities
200220-16:24:16,400 nipype.workflow DEBUG:
adding multipath trait: in_file
200220-16:24:16,400 nipype.workflow DEBUG:
adding multipath trait: entities
200220-16:24:16,401 nipype.workflow DEBUG:
adding multipath trait: in_file
200220-16:24:16,401 nipype.workflow DEBUG:
adding multipath trait: entities
200220-16:24:16,402 nipype.workflow DEBUG:
adding multipath trait: in_file
200220-16:24:16,402 nipype.workflow DEBUG:
(fitlins_wf.loader, fitlins_wf.ds_model_warning): No edge data
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.loader, fitlins_wf.ds_model_warning): new edge data: {'connect': [('warnings', 'in_file')]}
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.loader, fitlins_wf.design_matrix): No edge data
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.loader, fitlins_wf.design_matrix): new edge data: {'connect': [('design_info', 'session_info')]}
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.getter, fitlins_wf.design_matrix): No edge data
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.getter, fitlins_wf.design_matrix): new edge data: {'connect': [('bold_files', 'bold_file')]}
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.getter, fitlins_wf.l1_model): No edge data
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.getter, fitlins_wf.l1_model): new edge data: {'connect': [('bold_files', 'bold_file'), ('mask_files', 'mask_file')]}
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.l1_model): No edge data
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.l1_model): new edge data: {'connect': [('design_matrix', 'design_matrix')]}
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.plot_design): No edge data
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.plot_design): new edge data: {'connect': [('design_matrix', 'data')]}
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.plot_l1_contrast_matrix): No edge data
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.plot_l1_contrast_matrix): new edge data: {'connect': [('design_matrix', 'data')]}
200220-16:24:16,403 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.plot_corr): No edge data
200220-16:24:16,404 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.plot_corr): new edge data: {'connect': [('design_matrix', 'data')]}
200220-16:24:16,404 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.deindex_tsv): No edge data
200220-16:24:16,404 nipype.workflow DEBUG:
(fitlins_wf.design_matrix, fitlins_wf.deindex_tsv): new edge data: {'connect': [('design_matrix', 'tsv')]}
200220-16:24:16,404 nipype.workflow DEBUG:
(fitlins_wf.deindex_tsv, fitlins_wf.ds_design_matrix): No edge data
200220-16:24:16,404 nipype.workflow DEBUG:
(fitlins_wf.deindex_tsv, fitlins_wf.ds_design_matrix): new edge data: {'connect': [('out', 'in_file')]}
200220-16:24:16,405 nipype.workflow DEBUG:
adding multipath trait: data
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.loader, fitlins_wf.select_l1_entities): No edge data
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.loader, fitlins_wf.select_l1_entities): new edge data: {'connect': [('entities', 'inlist')]}
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.getter): No edge data
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.getter): new edge data: {'connect': [('out', 'entities')]}
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_model_warning): No edge data
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_model_warning): new edge data: {'connect': [('out', 'entities')]}
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_design): No edge data
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_design): new edge data: {'connect': [('out', 'entities')]}
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_design_matrix): No edge data
200220-16:24:16,407 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_design_matrix): new edge data: {'connect': [('out', 'entities')]}
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.plot_design, fitlins_wf.ds_design): No edge data
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.plot_design, fitlins_wf.ds_design): new edge data: {'connect': [('figure', 'in_file')]}
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.select_l1_contrasts, fitlins_wf.plot_l1_contrast_matrix): No edge data
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.select_l1_contrasts, fitlins_wf.plot_l1_contrast_matrix): new edge data: {'connect': [('out', 'contrast_info')]}
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.select_l1_contrasts, fitlins_wf.plot_corr): No edge data
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.select_l1_contrasts, fitlins_wf.plot_corr): new edge data: {'connect': [('out', 'contrast_info')]}
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_l1_contrasts): No edge data
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_l1_contrasts): new edge data: {'connect': [('out', 'entities')]}
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_corr): No edge data
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.select_l1_entities, fitlins_wf.ds_corr): new edge data: {'connect': [('out', 'entities')]}
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.plot_l1_contrast_matrix, fitlins_wf.ds_l1_contrasts): No edge data
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.plot_l1_contrast_matrix, fitlins_wf.ds_l1_contrasts): new edge data: {'connect': [('figure', 'in_file')]}
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.plot_corr, fitlins_wf.ds_corr): No edge data
200220-16:24:16,408 nipype.workflow DEBUG:
(fitlins_wf.plot_corr, fitlins_wf.ds_corr): new edge data: {'connect': [('figure', 'in_file')]}
200220-16:24:16,409 nipype.workflow DEBUG:
(fitlins_wf.loader, fitlins_wf.select_l1_contrasts): No edge data
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.loader, fitlins_wf.select_l1_contrasts): new edge data: {'connect': [('contrast_info', 'inlist')]}
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.select_l1_contrasts, fitlins_wf.l1_model): No edge data
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.select_l1_contrasts, fitlins_wf.l1_model): new edge data: {'connect': [('out', 'contrast_info')]}
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.l1_model, fitlins_wf.collate_l1): No edge data
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.l1_model, fitlins_wf.collate_l1): new edge data: {'connect': [('effect_maps', 'effect_maps'), ('variance_maps', 'variance_maps'), ('stat_ma
ps', 'stat_maps'), ('zscore_maps', 'zscore_maps'), ('pvalue_maps', 'pvalue_maps'), ('contrast_metadata', 'contrast_metadata')]}
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.collate_l1, fitlins_wf.collate_l1_outputs): No edge data
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.collate_l1, fitlins_wf.collate_l1_outputs): new edge data: {'connect': [('contrast_metadata', 'metadata'), ('effect_maps', 'effect_maps'),
('variance_maps', 'variance_maps'), ('stat_maps', 'stat_maps'), ('zscore_maps', 'zscore_maps'), ('pvalue_maps', 'pvalue_maps')]}
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.collate_l1, fitlins_wf.plot_l1_contrasts): No edge data
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.collate_l1, fitlins_wf.plot_l1_contrasts): new edge data: {'connect': [('stat_maps', 'data')]}
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.collate_l1_outputs, fitlins_wf.ds_l1_contrast_maps): No edge data
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.collate_l1_outputs, fitlins_wf.ds_l1_contrast_maps): new edge data: {'connect': [('out', 'in_file'), ('metadata', 'entities')]}
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.collate_l1, fitlins_wf.ds_l1_contrast_plots): No edge data
200220-16:24:16,410 nipype.workflow DEBUG:
(fitlins_wf.collate_l1, fitlins_wf.ds_l1_contrast_plots): new edge data: {'connect': [('contrast_metadata', 'entities')]}
200220-16:24:16,411 nipype.workflow DEBUG:
(fitlins_wf.plot_l1_contrasts, fitlins_wf.ds_l1_contrast_plots): No edge data
200220-16:24:16,411 nipype.workflow DEBUG:
(fitlins_wf.plot_l1_contrasts, fitlins_wf.ds_l1_contrast_plots): new edge data: {'connect': [('figure', 'in_file')]}
200220-16:24:16,437 nipype.workflow DEBUG:
[MultiProc] Starting (n_procs=72, mem_gb=452.68, cwd=/scratch/qbi/uqkgarn1)
200220-16:24:16,438 nipype.workflow DEBUG:
Creating flat graph for workflow: fitlins_wf
200220-16:24:16,443 nipype.workflow DEBUG:
expanding workflow: fitlins_wf
200220-16:24:16,444 nipype.workflow DEBUG:
processing node: fitlins_wf.loader
200220-16:24:16,444 nipype.workflow DEBUG:
processing node: fitlins_wf.select_l1_contrasts
200220-16:24:16,444 nipype.workflow DEBUG:
processing node: fitlins_wf.select_l1_entities
200220-16:24:16,444 nipype.workflow DEBUG:
processing node: fitlins_wf.ds_model_warning
200220-16:24:16,445 nipype.workflow DEBUG:
processing node: fitlins_wf.getter
200220-16:24:16,445 nipype.workflow DEBUG:
processing node: fitlins_wf.design_matrix
200220-16:24:16,445 nipype.workflow DEBUG:
processing node: fitlins_wf.deindex_tsv
200220-16:24:16,445 nipype.workflow DEBUG:
processing node: fitlins_wf.ds_design_matrix
200220-16:24:16,445 nipype.workflow DEBUG:
processing node: fitlins_wf.plot_corr
200220-16:24:16,445 nipype.workflow DEBUG:
processing node: fitlins_wf.ds_corr
200220-16:24:16,445 nipype.workflow DEBUG:
processing node: fitlins_wf.plot_l1_contrast_matrix
200220-16:24:16,445 nipype.workflow DEBUG:
processing node: fitlins_wf.ds_l1_contrasts
200220-16:24:16,446 nipype.workflow DEBUG:
processing node: fitlins_wf.plot_design
200220-16:24:16,446 nipype.workflow DEBUG:
processing node: fitlins_wf.ds_design
200220-16:24:16,446 nipype.workflow DEBUG:
processing node: fitlins_wf.l1_model
200220-16:24:16,446 nipype.workflow DEBUG:
processing node: fitlins_wf.collate_l1
200220-16:24:16,446 nipype.workflow DEBUG:
processing node: fitlins_wf.plot_l1_contrasts
200220-16:24:16,446 nipype.workflow DEBUG:
processing node: fitlins_wf.ds_l1_contrast_plots
200220-16:24:16,446 nipype.workflow DEBUG:
processing node: fitlins_wf.collate_l1_outputs
200220-16:24:16,446 nipype.workflow DEBUG:
processing node: fitlins_wf.ds_l1_contrast_maps
200220-16:24:16,446 nipype.workflow DEBUG:
finished expanding workflow: fitlins_wf
200220-16:24:16,446 nipype.workflow INFO:
Workflow fitlins_wf settings: ['check', 'execution', 'logging', 'monitoring']
200220-16:24:16,451 nipype.workflow DEBUG:
PE: expanding iterables
200220-16:24:16,451 nipype.workflow DEBUG:
Detected iterable nodes []
200220-16:24:16,451 nipype.workflow DEBUG:
PE: expanding iterables ... done
200220-16:24:16,459 nipype.workflow DEBUG:
Performing depth first search
200220-16:24:16,463 nipype.workflow INFO:
Running in parallel.
200220-16:24:16,468 nipype.workflow DEBUG:
Progress: 20 jobs, 0/0/1 (done/running/ready), 0/20 (pending_tasks/waiting).
200220-16:24:16,468 nipype.workflow DEBUG:
Tasks currently running: 0. Pending: 0.
200220-16:24:16,469 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 452.68/452.68, Free processors: 72/72.
200220-16:24:16,537 nipype.workflow DEBUG:
Allocating fitlins_wf.loader ID=0 (0.20GB, 1 threads). Free: 452.48GB, 71 threads.
200220-16:24:16,538 nipype.workflow DEBUG:
[Node] Hashes: [('database_path', '/scratch/qbi/uqkgarn1/work/dbcache'), ('model', [('Description', 'model to remove variance due to movement for tSNR
- TR 1510'), ('Input', [('TR', 1510), ('task', 'learnAtt')]), ('Name', 'mc_wp1_move_TR_1510'), ('Steps', [[('Level', 'run'), ('Model', [('X', ['framewise_displa
cement', 'trans_x', 'trans_x_derivative1', 'trans_y', 'trans_y_derivative1', 'trans_z', 'trans_z_derivative1', 'rot_x', 'rot_x_derivative1', 'rot_y', 'rot_y_der
ivative1', 'rot_z', 'rot_z_derivative1'])])]])]), ('selectors', [('desc', 'preproc'), ('space', 'MNI152NLin2009cAsym')]), ('needed_outputs', ['contrast_info', '
design_info', 'entities', 'warnings'])], 8f1a51cee538bcfe47dda33d73f9cdd2, /scratch/qbi/uqkgarn1/work/fitlins_wf/loader/_0x8f1a51cee538bcfe47dda33d73f9cdd2.json
, []
200220-16:24:16,538 nipype.workflow DEBUG:
[Node] No hashfiles found in "/scratch/qbi/uqkgarn1/work/fitlins_wf/loader".
200220-16:24:16,538 nipype.workflow DEBUG:
Checking hash "fitlins_wf.loader" locally: cached=False, updated=False.
200220-16:24:16,799 nipype.workflow DEBUG:
[MultiProc] Submitted task fitlins_wf.loader (taskid=1).
200220-16:24:16,805 nipype.workflow INFO:
[Node] Setting-up "fitlins_wf.loader" in "/scratch/qbi/uqkgarn1/work/fitlins_wf/loader".
200220-16:24:16,805 nipype.workflow DEBUG:
[Node] Hashes: [('database_path', '/scratch/qbi/uqkgarn1/work/dbcache'), ('model', [('Description', 'model to remove variance due to movement for tSNR
- TR 1510'), ('Input', [('TR', 1510), ('task', 'learnAtt')]), ('Name', 'mc_wp1_move_TR_1510'), ('Steps', [[('Level', 'run'), ('Model', [('X', ['framewise_displa
cement', 'trans_x', 'trans_x_derivative1', 'trans_y', 'trans_y_derivative1', 'trans_z', 'trans_z_derivative1', 'rot_x', 'rot_x_derivative1', 'rot_y', 'rot_y_der
ivative1', 'rot_z', 'rot_z_derivative1'])])]])]), ('selectors', [('desc', 'preproc'), ('space', 'MNI152NLin2009cAsym')]), ('needed_outputs', ['contrast_info', '
design_info', 'entities', 'warnings'])], 8f1a51cee538bcfe47dda33d73f9cdd2, /scratch/qbi/uqkgarn1/work/fitlins_wf/loader/_0x8f1a51cee538bcfe47dda33d73f9cdd2.json
, []
200220-16:24:16,805 nipype.workflow DEBUG:
[Node] No hashfiles found in "/scratch/qbi/uqkgarn1/work/fitlins_wf/loader".
200220-16:24:16,806 nipype.utils DEBUG:
Removing contents of /scratch/qbi/uqkgarn1/work/fitlins_wf/loader
200220-16:24:16,808 nipype.workflow DEBUG:
[Node] Writing pre-exec report to "/scratch/qbi/uqkgarn1/work/fitlins_wf/loader/_report/report.rst"
200220-16:24:16,813 nipype.workflow INFO:
[Node] Running "loader" ("fitlins.interfaces.bids.LoadBIDSModel")
200220-16:24:18,470 nipype.workflow DEBUG:
Progress: 20 jobs, 0/1/0 (done/running/ready), 1/19 (pending_tasks/waiting).
200220-16:24:18,470 nipype.workflow DEBUG:
Tasks currently running: 1. Pending: 1.
200220-16:24:18,471 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 452.48/452.68, Free processors: 71/72.
Currently running:
* fitlins_wf.loader
200220-16:31:16,906 nipype.workflow DEBUG:
Saving results file: '/scratch/qbi/uqkgarn1/work/fitlins_wf/loader/result_loader.pklz'
200220-16:31:16,906 nipype.workflow WARNING:
Storing result file without outputs
200220-16:31:16,907 nipype.workflow WARNING:
[Node] Error on "fitlins_wf.loader" (/scratch/qbi/uqkgarn1/work/fitlins_wf/loader)
200220-16:31:16,908 nipype.utils DEBUG:
Loading pkl: /scratch/qbi/uqkgarn1/work/fitlins_wf/loader/result_loader.pklz
200220-16:31:18,894 nipype.workflow DEBUG:
Clearing 0 from queue
200220-16:31:18,896 nipype.utils DEBUG:
Loading pkl: /scratch/qbi/uqkgarn1/work/fitlins_wf/loader/result_loader.pklz
200220-16:31:18,897 nipype.workflow ERROR:
Node loader failed to run on host inode2.hpc.dc.uq.edu.au.
200220-16:31:18,897 nipype.workflow ERROR:
Saving crash info to /scratch/qbi/uqkgarn1/work/crash-20200220-163118-uqkgarn1-loader-7029ecd2-01e2-4daa-96e2-fb9669444a48.txt
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 479, in run
result = self._run_interface(execute=True)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 585, in _run_interface
return self._run_command(execute)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 678, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 382, in run
runtime = self._run_interface(runtime)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/fitlins/interfaces/bids.py", line 212, in _run_interface
analysis.setup(drop_na=False, **selectors)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 94, in setup
b.setup(input_nodes, drop_na=drop_na, **selectors)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 207, in setup
**kwargs)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/layout/layout.py", line 1097, in get_collections
return index.get_collections(level, variables, merge,
AttributeError: 'RunNode' object has no attribute 'get_collections'
200220-16:31:18,898 nipype.workflow DEBUG:
Tasks currently running: 0. Pending: 0.
200220-16:31:18,899 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 452.68/452.68, Free processors: 72/72.
200220-16:31:18,899 nipype.workflow DEBUG:
No tasks are being run, and no jobs can be submitted to the queue. Potential deadlock
200220-16:31:20,895 nipype.workflow INFO:
***********************************
200220-16:31:20,895 nipype.workflow ERROR:
could not run node: fitlins_wf.loader
200220-16:31:20,896 nipype.workflow INFO:
crashfile: /scratch/qbi/uqkgarn1/work/crash-20200220-163118-uqkgarn1-loader-7029ecd2-01e2-4daa-96e2-fb9669444a48.txt
200220-16:31:20,896 nipype.workflow DEBUG:
The following dependent nodes were not run
200220-16:31:20,896 nipype.workflow DEBUG:
loader
200220-16:31:20,896 nipype.workflow DEBUG:
ds_model_warning
200220-16:31:20,896 nipype.workflow DEBUG:
design_matrix
200220-16:31:20,896 nipype.workflow DEBUG:
l1_model
200220-16:31:20,896 nipype.workflow DEBUG:
collate_l1
200220-16:31:20,896 nipype.workflow DEBUG:
collate_l1_outputs
200220-16:31:20,896 nipype.workflow DEBUG:
ds_l1_contrast_maps
200220-16:31:20,896 nipype.workflow DEBUG:
plot_l1_contrasts
200220-16:31:20,896 nipype.workflow DEBUG:
ds_l1_contrast_plots
200220-16:31:20,896 nipype.workflow DEBUG:
plot_design
200220-16:31:20,896 nipype.workflow DEBUG:
ds_design
200220-16:31:20,896 nipype.workflow DEBUG:
plot_l1_contrast_matrix
200220-16:31:20,896 nipype.workflow DEBUG:
ds_l1_contrasts
200220-16:31:20,896 nipype.workflow DEBUG:
plot_corr
200220-16:31:20,897 nipype.workflow DEBUG:
ds_corr
200220-16:31:20,897 nipype.workflow DEBUG:
deindex_tsv
200220-16:31:20,897 nipype.workflow DEBUG:
ds_design_matrix
200220-16:31:20,897 nipype.workflow DEBUG:
select_l1_entities
200220-16:31:20,897 nipype.workflow DEBUG:
getter
200220-16:31:20,897 nipype.workflow DEBUG:
select_l1_contrasts
200220-16:31:20,897 nipype.workflow INFO:
***********************************
Traceback (most recent call last):
File "/opt/miniconda-latest/envs/neuro/bin/fitlins", line 8, in <module>
sys.exit(main())
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/fitlins/cli/run.py", line 272, in main
sys.exit(run_fitlins(sys.argv[1:]))
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/fitlins/cli/run.py", line 264, in run_fitlins
analysis.setup(**selectors)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 94, in setup
b.setup(input_nodes, drop_na=drop_na, **selectors)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/analysis/analysis.py", line 207, in setup
**kwargs)
File "/opt/miniconda-latest/envs/neuro/lib/python3.6/site-packages/bids/layout/layout.py", line 1097, in get_collections
return index.get_collections(level, variables, merge,