[RF] Remove the recon workflows from QSIPrep

[mattcieslak]

Closes #697.

It's difficult to maintain the recon workflows and preprocessing workflows in one package. We're creating a separate package that takes QSIPrep (or UKBB) preprocessed data and runs the recon workflows on it. The new QSIRecon repo can be found here.

For users this means that the following options will no longer be available from qsiprep:

• --recon-only
• --recon-spec
• --recon-input
• --recon-input-pipeline
• --freesurfer-input
• --skip-odf-reports
• --interactive-reports-only

And because preprocessing doesn't directly use freesurfer, we don't need

• --fs-license-file

Also, QSIPrep will no longer append qsiprep to the output directory.

[tsalo]

When I disabled test_main, I got the weirdest error:

Cmdline:
	dsi_studio --action=rec --method=4 --align_acpc=0 --check_btable=0 --dti_no_high_b=1 --source=/src/qsiprep/.circleci/work/dscsdsi/qsiprep_0_22_wf/sub_tester_wf/dwi_preproc_acq_HASC55AP_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_qc_wf/raw_gqi/sub-tester_acq-HASC55AP_dwi_merged.src.gz --num_fiber=3 --thread_count=8 --other_output=all --record_odf=1 --r2_weighted=0 --param0=1.2500 --thread_count=8
Stdout:
	DSI Studio version: Hou "侯" Aug  2 2024
	┌──�[1;34m📟command line�[0m
	├──�[0;32msource�[0m=/src/qsiprep/.circleci/work/dscsdsi/qsiprep_0_22_wf/sub_tester_wf/dwi_preproc_acq_HASC55AP_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_qc_wf/raw_gqi/sub-tester_acq-HASC55AP_dwi_merged.src.gz
	├──�[0;32maction�[0m=rec
	├──�[0;32mloop�[0m=/src/qsiprep/.circleci/work/dscsdsi/qsiprep_0_22_wf/sub_tester_wf/dwi_preproc_acq_HASC55AP_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_qc_wf/raw_gqi/sub-tester_acq-HASC55AP_dwi_merged.src.gz
	├──┬──�[1;34m📟run rec�[0m
	│  ├──┬──�[1;35m📂open SRC file sub-tester_acq-HASC55AP_dwi_merged.src.gz�[0m
	│  │  ├──generating mask
	│  │  └──⏱49ms
	│  ├──┬──�[1;34m📟reconstruction parameters�[0m
	│  │  ├──�[0;32mmethod�[0m=4
	│  │  ├──�[0;32modf_resolving�[0m=0
	│  │  ├──�[0;32mrecord_odf�[0m=1
	│  │  ├──�[0;32mdti_no_high_b�[0m=1
	│  │  ├──�[0;32mother_output�[0m=all
	│  │  ├──�[0;32mr2_weighted�[0m=0
	│  │  ├──�[0;32mthread_count�[0m=8
	│  │  ├──�[0;32mparam0�[0m=1.2500
	│  │  ├──�[0;32mparam1�[0m=3000
	│  │  ├──�[0;32mparam2�[0m=0.05
	│  │  ├──�[0;33mtemplate 0�[0m: "ICBM152_adult.QA.nii"
	│  │  ├──�[0;33mtemplate 1�[0m: "C57BL6_mouse.QA.nii"
	│  │  ├──�[0;33mtemplate 2�[0m: "dHCP_neonate.QA.nii"
	│  │  ├──�[0;33mtemplate 3�[0m: "INDI_rhesus.QA.nii"
	│  │  ├──�[0;33mtemplate 4�[0m: "Pitt_marmoset.QA.nii"
	│  │  ├──�[0;33mtemplate 5�[0m: "WHS_SD_rat.QA.nii"
	│  │  ├──�[0;32mtemplate�[0m=0
	│  │  └──⏱0ms
	│  ├──�[0;32mmask�[0m=1
	│  ├──┬──�[1;34m📟pre-processing steps�[0m
	│  │  ├──�[0;32mmotion_correction�[0m=0
	│  │  ├──�[0;32mcheck_btable�[0m=0
	│  │  ├──�[0;32malign_acpc�[0m=0
	│  │  └──⏱0ms
	│  ├──┬──�[1;34m📟pre-reconstruction�[0m
	│  │  ├──11ReadDWIData
	│  │  ├──10Dwi2Tensor
	│  │  ├──9GQI_Recon
	│  │  ├──9RDI_Recon
	│  │  ├──11SaveMetrics
	│  │  ├──9OutputODF
	│  │  └──⏱46ms
	│  ├──┬──�[1;34m📟GQI�[0m
	│  │  └──⏱158ms
	│  ├──┬──�[1;34m📟post-reconstruction�[0m
	│  │  ├──11ReadDWIData
	│  │  ├──10Dwi2Tensor
	│  │  ├──9GQI_Recon
	│  │  ├──9RDI_Recon
	│  │  ├──11SaveMetrics
	│  │  ├──9OutputODF
	│  │  ├──┬──�[1;34m📟odf�[0m
	│  │  │  └──⏱1.25s
	│  │  └──⏱1.362s
	│  ├──�[1;35m💾saving /src/qsiprep/.circleci/work/dscsdsi/qsiprep_0_22_wf/sub_tester_wf/dwi_preproc_acq_HASC55AP_wf/pre_hmc_wf/merge_and_denoise_wf/dwi_qc_wf/raw_gqi/sub-tester_acq-HASC55AP_dwi_merged.src.gz.odf.gqi.1.25.fib.gz�[0m
	│  └──⏱1.618s
	└──⏱1.62s
	�[1;31m❗--num_fiber is not used/recognized. Did you mean --stay_open ?�[0m
	�[1;31m❗--thread_count is not used/recognized. Did you mean --other_image ?�[0m
Stderr:

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 400, in run
	    outputs = self.aggregate_outputs(runtime)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 429, in aggregate_outputs
	    predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
	  File "/src/qsiprep/qsiprep/interfaces/dsi_studio.py", line 235, in _list_outputs
	    config.loggers.interface.info("current dir", os.getcwd())
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1477, in info
	    self._log(INFO, msg, args, **kwargs)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1624, in _log
	    self.handle(record)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1634, in handle
	    self.callHandlers(record)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1696, in callHandlers
	    hdlr.handle(record)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 968, in handle
	    self.emit(record)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/_pytest/logging.py", line 388, in emit
	    super().emit(record)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1108, in emit
	    self.handleError(record)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 1100, in emit
	    msg = self.format(record)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 943, in format
	    return fmt.format(record)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/_pytest/logging.py", line 141, in format
	    return super().format(record)
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 678, in format
	    record.message = record.getMessage()
	  File "/opt/conda/envs/qsiprep/lib/python3.10/logging/__init__.py", line 368, in getMessage
	    msg = msg % self.args
	TypeError: not all arguments converted during string formatting

[mattcieslak]

This is from a bad call to the logger in interfaces/dsi_studio.py. There were a couple other instances in there that I fixed, but it switched from a print (that allowed multiple arguments) to a logger.info, where it is expecting the second and later arguments to be used in formatting the first

[tsalo]

It's still really weird that the way I run the tests affects it. I'll have to dig into that in a follow-up PR.

[mattcieslak]

I was wondering about that too. qsiprep will print the error but exit with a 0 status

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 59.30233% with 35 lines in your changes missing coverage. Please review.

Project coverage is 28.59%. Comparing base (7506edb) to head (302f030).

Files	Patch %	Lines
qsiprep/workflows/anatomical/surface.py	0.00%	6 Missing ⚠️
qsiprep/workflows/anatomical/volume.py	14.28%	6 Missing ⚠️
qsiprep/cli/workflow.py	20.00%	4 Missing ⚠️
qsiprep/utils/misc.py	0.00%	4 Missing ⚠️
qsiprep/workflows/base.py	0.00%	3 Missing ⚠️
qsiprep/cli/run.py	71.42%	2 Missing ⚠️
qsiprep/interfaces/bids.py	92.00%	2 Missing ⚠️
qsiprep/workflows/dwi/finalize.py	0.00%	2 Missing ⚠️
qsiprep/workflows/fieldmap/unwarp.py	0.00%	2 Missing ⚠️
qsiprep/interfaces/dipy.py	0.00%	1 Missing ⚠️
... and 3 more

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #802      +/-   ##
==========================================
- Coverage   29.86%   28.59%   -1.27%     
==========================================
  Files          97       69      -28     
  Lines       14627    10218    -4409     
  Branches     1892     1331     -561     
==========================================
- Hits         4368     2922    -1446     
+ Misses      10126     7195    -2931     
+ Partials      133      101      -32     

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