QSIRecon: NameError: name 'has_qsiprep_t1w' is not defined

[smeisler]

Summary

When starting a recon workflow (HSVS tractography --> pyafq and scaler production) I get an error when logging what anatomical inputs are available.

Additional details

• QSIPrep 0.20.0
• Apptainer 1.1.7

What actually happened?

    Running qsirecon version 0.20.1.dev0+geda84d5.d20240112:
      * BIDS dataset path: /om2/scratch/tmp/smeisler/fsub_proc/sub-01/data.
      * Participant list: ['01'].
      * Run identifier: 20240228-215923_25b787db-62e3-47fc-bb80-ffa9d166b8ac.
    
240228-21:59:29,67 nipype.workflow INFO:
	 found ['/om2/scratch/tmp/smeisler/fsub_proc/sub-01/data/derivatives/qsiprep/sub-01/dwi/sub-01_space-T1w_desc-preproc_dwi.nii.gz'] in /om2/scratch/tmp/smeisler/fsub_proc/sub-01/data/derivatives/qsiprep
240228-21:59:29,74 nipype.workflow WARNING:
	 A Non-gzipped input nifti file was found. Consider gzipping /om2/scratch/tmp/smeisler/fsub_proc/sub-01/data/derivatives/qsiprep/sub-01/anat/sub-01_desc-preproc_T1w.nii
240228-21:59:29,74 nipype.workflow INFO:
	 Found usable QSIPrep-preprocessed T1w image and mask.
240228-21:59:29,77 nipype.workflow INFO:
	 Found high-res anatomical data in preprocessed inputs for 01.
240228-21:59:29,78 nipype.workflow INFO:
	 Freesurfer directory /om2/scratch/tmp/smeisler/fsub_proc/sub-01/data/derivatives/freesurfer/sub-01 exists for 01
240228-21:59:29,82 nipype.workflow INFO:
	 FreeSurfer data will be used to create a HSVS 5tt image.
Process Process-36:
Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/cli/run.py", line 1198, in build_recon_workflow
    retval['workflow'] = init_qsirecon_wf(
  File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/workflows/recon/base.py", line 99, in init_qsirecon_wf
    single_subject_wf = init_single_subject_wf(
  File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/workflows/recon/base.py", line 208, in init_single_subject_wf
    anat_ingress_node, available_anatomical_data = init_highres_recon_anatomical_wf(
  File "/usr/local/miniconda/lib/python3.10/site-packages/qsiprep/workflows/recon/anatomical.py", line 162, in init_highres_recon_anatomical_wf
    if has_qsiprep_t1w:
NameError: name 'has_qsiprep_t1w' is not defined

Reproducing the bug

QSIPrep CMD

singularity run -e --containall -B $scratch,$templateflow $IMG \
$scratch/data/ $scratch/data/derivatives participant \
--participant_label $SUB \
-w $scratch \
--output_resolution 1.25 \
--unringing-method mrdegibbs \
--recon-spec $scratch/recon_spec.json \
--freesurfer-input $scratch/data/derivatives/freesurfer/ \
--fs-license-file $scratch/license.txt \
--skip-odf-reports \
--notrack \
--mem_mb 239000 \
--nthreads 32 \
--omp-nthreads 8 \

Recon spec

{
"name": "mrtrix_multishell_msmt_hsvs_pyafq_tractometry",
"space": "T1w",
"atlases": [],
"anatomical": [
	"mrtrix_5tt_hsvs"
],
"nodes": [{
		"name": "msmt_csd",
		"software": "MRTrix3",
		"action": "csd",
		"output_suffix": "msmtcsd",
		"input": "qsiprep",
		"parameters": {
			"mtnormalize": true,
			"response": {
				"algorithm": "dhollander"
			},
			"fod": {
				"algorithm": "msmt_csd",
				"max_sh": [8, 8, 8]
			}
		}
	},
	{
		"name": "track_ifod2",
		"software": "MRTrix3",
		"action": "tractography",
		"output_suffix": "ifod2",
		"input": "msmt_csd",
		"parameters": {
			"use_5tt": true,
			"method_5tt": "hsvs",
			"use_sift2": true,
			"tckgen": {
				"algorithm": "iFOD2",
				"select": 1e7,
				"max_length": 250,
				"min_length": 30,
				"power": 0.33,
				"crop_at_gmwmi": true,
				"backtrack": true,
				"quiet": true
			},
			"sift2": {}
		}
	},
	{
		"name": "pyafq_tractometry",
		"software": "pyAFQ",
		"action": "pyafq_tractometry",
		"input": "track_ifod2",
		"output_suffix": "PYAFQ_TRACTOMETRY_ET",
		"parameters": {
			"use_external_tracking": true,
			"export": "all",
			"directions": "prob",
			"max_angle": 30.0,
			"sphere": "",
			"seed_mask": "",
			"seed_threshold": 0,
			"n_seeds": 1,
			"random_seeds": false,
			"rng_seed": "",
			"stop_mask": "",
			"stop_threshold": 0,
			"step_size": 0.5,
			"min_length": 50,
			"max_length": 250,
			"odf_model": "CSD",
			"tracker": "local",
			"nb_points": false,
			"nb_streamlines": false,
			"seg_algo": "AFQ",
			"reg_algo": "",
			"clip_edges": false,
			"parallel_segmentation": "{'n_jobs': -1, 'engine': 'joblib', 'backend': 'loky'}",
			"progressive": true,
			"greater_than": 50,
			"rm_small_clusters": 50,
			"model_clust_thr": 1.25,
			"reduction_thr": 25,
			"refine": false,
			"pruning_thr": 12,
			"b0_threshold": 50,
			"prob_threshold": 0,
			"roi_dist_tie_break": false,
			"dist_to_waypoint": "",
			"rng": "",
			"return_idx": false,
			"presegment_bundle_dict": "",
			"presegment_kwargs": "{}",
			"filter_by_endpoints": true,
			"dist_to_atlas": 4,
			"save_intermediates": "",
			"n_points": 100,
			"clean_rounds": 5,
			"distance_threshold": 3,
			"length_threshold": 4,
			"min_sl": 20,
			"stat": "mean",
			"min_bval": "",
			"max_bval": "",
			"filter_b": true,
			"robust_tensor_fitting": false,
			"csd_response": "",
			"csd_sh_order": "",
			"csd_lambda_": 1,
			"csd_tau": 0.1,
			"gtol": 0.01,
			"brain_mask_definition": "",
			"bundle_info": "",
			"reg_template_spec": "mni_T1",
			"mapping_definition": "",
			"reg_subject_spec": "power_map",
			"profile_weights": "gauss",
			"scalars": "['dki_fa', 'dki_md']",
			"import_tract": "",
			"sbv_lims_bundles": "[None, None]",
			"volume_opacity_bundles": 0.3,
			"n_points_bundles": 40,
			"sbv_lims_indiv": "[None, None]",
			"volume_opacity_indiv": 0.3,
			"n_points_indiv": 40,
			"viz_backend_spec": "plotly_no_gif",
			"virtual_frame_buffer": false
		}
	},
	{
		"name": "fit_noddi",
		"action": "fit_noddi",
		"software": "AMICO",
		"input": "qsiprep",
		"output_suffix": "NODDI",
		"parameters": {
			"isExvivo": false,
			"dPar": 1.7E-3,
			"dIso": 3.0E-3
		}
	},
	{
		"name": "dki_recon",
		"software": "Dipy",
		"action": "DKI_reconstruction",
		"input": "qsiprep",
		"output_suffix": "DKI",
		"parameters": {
			"write_mif": false,
			"write_fibgz": false
		}
	},
	{
		"name": "dsistudio_gqi",
		"software": "DSI Studio",
		"action": "reconstruction",
		"input": "qsiprep",
		"output_suffix": "gqi",
		"parameters": {
			"method": "gqi"
		}
	},
	{
		"name": "scalar_export",
		"software": "DSI Studio",
		"action": "export",
		"input": "dsistudio_gqi",
		"output_suffix": "gqiscalar"
	},
	{
		"name": "autotrackgqi",
		"software": "DSI Studio",
		"action": "autotrack",
		"input": "dsistudio_gqi",
		"output_suffix": "AutoTrackGQI",
		"parameters": {
			"track_id": "Fasciculus,Cingulum,Aslant,Corticos,Thalamic_R,Reticular,Optic,Fornix,Corpus",
			"tolerance": "22,26,30",
			"track_voxel_ratio": 2.0,
			"yield_rate": 0.000001
		}
	}
]
}

My diagnosis

I know that file has changed in recent commits but it looks like, at least at the release of 0.20.0, has_qsiprep_t1w was not defined in def init_highres_recon_anatomical_wf, and was only defined in the def gather_qsiprep_anatomical_data function. In earlier commits (e.g., 8ee6440), the input gathering was done in init_highres_recon_anatomical_wf, which might be why the error is popping up now.

Thanks,
Steven

[mattcieslak]

I just ran into this one too, thanks for opening the issue

[tsalo]

Seems related to #675 as well.

[mattcieslak]

Does anyone on this thread know of a good open dataset that has dwi and freesurfer results? The reason this exists as a bug now is that I don't have any good testing data for the hsvs workflow

[smeisler]

I have bids-ified one subject of the Natural Scenes Dataset, found here: (edit to remove link) I also have qsiprep outputs for it already, so you can go right to qsirecon testing.

[mattcieslak]

this is perfect! Do you mind if I use this in the CI tests?

[smeisler]

Don't mind at all!

[smeisler]

You should sign the data access agreement, though: https://docs.google.com/forms/d/e/1FAIpQLSduTPeZo54uEMKD-ihXmRhx0hBDdLHNsVyeo_kCb8qbyAkXuQ/viewform

[mattcieslak]

You're allowed to host the data on openneuro even with point 3 I will not distribute this dataset or its components to any other individual or entity?

[arokem]

I think HBN has these. Freesurfer v6 though

…

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