remove references to recon

.circleci/AllFieldmaps.sh

@@ -5,14 +5,13 @@ cat << DOC
 AllFieldmaps test
 =================
 
-Instead of running full workflows, this test checks that workflows can 
+Instead of running full workflows, this test checks that workflows can
 be built for all sorts of fieldmap configurations.
 
 This tests the following features:
  - Blip-up + Blip-down DWI series for TOPUP/Eddy
  - Eddy is run on a CPU
  - Denoising is skipped
- - A follow-up reconstruction using the dsi_studio_gqi workflow
 
 Inputs:
 -------

.circleci/DSDTI_TOPUP.sh

@@ -9,7 +9,6 @@ This tests the following features:
  - TOPUP on a single-shell sequence
  - Eddy is run on a CPU
  - mrdegibbs is run
- - A follow-up reconstruction using the dsi_studio_gqi workflow
 
 Inputs:
 -------
@@ -41,7 +40,6 @@ ${QSIPREP_CMD} \
 	--sloppy \
 	--unringing-method mrdegibbs \
 	--b1-biascorrect-stage legacy \
-	--recon-spec dsi_studio_gqi \
 	--eddy_config ${EDDY_CFG} \
 	--output-resolution 5 \
     -vv

.circleci/DSDTI_nofmap.sh

@@ -9,7 +9,6 @@ This tests the following features:
  - A workflow with no distortion correction followed by eddy
  - Eddy is run on a CPU
  - Denoising is skipped
- - A follow-up reconstruction using the dsi_studio_gqi workflow
 
 Inputs:
 -------

.circleci/DSDTI_outputs.txt

@@ -46,72 +46,4 @@ qsiprep/sub-PNC/figures/sub-PNC_acq-realistic_sampling_scheme.gif
 qsiprep/sub-PNC/figures/sub-PNC_seg_brainmask.svg
 qsiprep/sub-PNC/figures/sub-PNC_t1_2_mni.svg
 qsiprep/sub-PNC.html
-qsirecon
-qsirecon/dwiqc.json
-qsirecon/logs
-qsirecon/logs/CITATION.html
-qsirecon/logs/CITATION.md
-qsirecon/logs/CITATION.tex
-qsirecon/sub-PNC
-qsirecon/sub-PNC/dwi
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aal116_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aal116_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aal116_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aal116_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-ad_gqiscalar.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aicha384_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aicha384_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aicha384_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-aicha384_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-brainnetome246_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-brainnetome246_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-brainnetome246_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-brainnetome246_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-dti_fa_gqiscalar.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-fa0_gqiscalar.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-fa1_gqiscalar.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-fa2_gqiscalar.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gfa_gqiscalar.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gordon333_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gordon333_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gordon333_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-gordon333_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-iso_gqiscalar.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-md_gqiscalar.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-power264_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-power264_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-power264_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-power264_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-rd_gqiscalar.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x17_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x17_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x17_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x17_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x7_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x7_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x7_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer100x7_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x17_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x17_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x17_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x17_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x7_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x7_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x7_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer200x7_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x17_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x17_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x17_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x17_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x7_atlas.mif.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x7_atlas.nii.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x7_mrtrixLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-schaefer400x7_origLUT.txt
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_gqi.fib.gz
-qsirecon/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_gqinetwork.mat
-qsirecon/sub-PNC/figures
-qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-DSIStudioConnectivity_matrices.svg
-qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-GQIODF_odfs.png
-qsirecon/sub-PNC/figures/sub-PNC_acq-realistic_space-T1w_desc-preproc_space-T1w_desc-GQIODF_peaks.png
-qsirecon/sub-PNC.html
 /tmp/DSDTI/derivatives

.circleci/DSDTI_synfmap.sh

@@ -9,7 +9,6 @@ This tests the following features:
  - A workflow with no distortion correction followed by eddy
  - Eddy is run on a CPU
  - Denoising is skipped
- - A follow-up reconstruction using the dsi_studio_gqi workflow
 
 Inputs:
 -------

.circleci/config.yml

@@ -525,109 +525,76 @@ workflows:
           requires:
             - download_DSCSDSI
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - DRBUDDI_SHORELine_EPI:
           requires:
             - download_drbuddi_epi
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - DRBUDDI_eddy_rpe_series:
           requires:
             - download_drbuddi_rpe_series
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - DRBUDDI_TENSORLine_EPI:
           requires:
             - download_DSDTI
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - DSDTI_nofmap:
           requires:
             - download_DSDTI
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - DSDTI_synfmap:
           requires:
             - download_DSDTI
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - DSDTI_TOPUP:
           requires:
             - download_DSDTI
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - maternal_brain_project:
           requires:
             - build
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - forrest_gump:
           requires:
             - build
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - IntramodalTemplate:
           requires:
             - build
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 
       - MultiT1w:
           requires:
             - download_twoses
           filters:
-            branches:
-              ignore:
-                - /recon\/.*/
             tags:
               only: /.*/
 

long_description.rst

@@ -7,9 +7,4 @@ gradient direction and strength.
 Since qsiprep uses the FMRIPREP workflow-building strategy, it can also generate methods
 boilerplate and quality-check figures.
 
-Users can also reconstruct orientation distribution functions (ODFs), fiber orientation
-distributions (FODs) and perform tractography, estimate anisotropy scalars and connectivity
-estimation using a combination of Dipy, MRTrix and DSI Studio using a JSON-based pipeline
-specification.
-
 [Documentation `qsiprep.org <https://qsiprep.readthedocs.io>`_]

pyproject.toml

@@ -85,10 +85,6 @@ all = ["qsiprep[doc,maint,tests]"]
 
 [project.scripts]
 qsiprep = "qsiprep.cli.run:main"
-mif2fib = "qsiprep.cli.convertODFs:mif_to_fib"
-fib2mif = "qsiprep.cli.convertODFs:fib_to_mif"
-qsiprep_group_report = "qsiprep.cli.group_report:aggregate_reports"
-recon_plot = "qsiprep.cli.recon_plot:recon_plot"
 
 #
 # Hatch configurations
@@ -169,14 +165,10 @@ per-file-ignores = [
 addopts = '-m "not integration"'
 markers = [
     "integration: integration tests to skip by default",
-    "mrtrix_singleshell_ss3t_act: test 1",
-    "mrtrix_singleshell_ss3t_noact: test 2",
     "dsdti_fmap: test 3",
     "dscsdsi_fmap: test 4",
     "amico_noddi: test 5",
     "cuda: test 6",
-    "dipy_mapmri: test 7",
-    "dipy_dki: test 8",
     "drbuddi_rpe: test 9",
     "drbuddi_shoreline_epi: test 10",
     "drbuddi_tensorline_epi: test 11",
@@ -185,11 +177,6 @@ markers = [
     "dsdti_synfmap: test 14",
     "dsdti_topup: test 15",
     "intramodal_template: test 16",
-    "scalar_mapper: test 17",
-    "pyafq_recon_external_trk: test 18",
-    "pyafq_recon_full: test 19",
-    "mrtrix3_recon: test 20",
-    "tortoise_recon: test 21",
     "multi_t1w: test 22",
     "maternal_brain_project: multi-shell with GRE field map",
     "forrest_gump: single-shell with GRE field map",

qsiprep/cli/parser.py

@@ -44,9 +44,7 @@ def _build_parser(**kwargs):
         # parser attribute name: (replacement flag, version slated to be removed in)
         "dwi_only": ("--anat-modality none", "0.23.0"),
         "prefer_dedicated_fmaps": (None, "0.23.0"),
-        "do_reconall": (None, "0.23.0"),
         "dwi_no_biascorr": ("--b1-biascorrect-stage none", "0.23.0"),
-        "recon_only": (None, "0.23.0"),
         "b0_motion_corr_to": (None, "0.23.0"),
         "b0_to_t1w_transform": ("--b0-t0-anat-transform", "0.23.0"),
     }
@@ -323,7 +321,7 @@ def _bids_filter(value, parser):
         default="T1w",
         help="Modality to use as the anatomical reference. Images of this "
         "contrast will be skull stripped and segmented for use in the "
-        "visual reports and reconstruction. If --infant, T2w is forced.",
+        "visual reports. If --infant, T2w is forced.",
     )
     g_conf.add_argument(
         "--b0-threshold",
@@ -423,8 +421,7 @@ def _bids_filter(value, parser):
         "--output-resolution",
         "--output_resolution",
         action="store",
-        # required when not recon-only (which can be specified in sysargs 2 ways)
-        required=not any(rcn in sys.argv for rcn in ["--recon-only", "--recon_only"]),
+        required=True,
         type=float,
         help="the isotropic voxel size in mm the data will be resampled to "
         "after preprocessing. If set to a lower value than the original voxel "
@@ -685,11 +682,6 @@ def parse_args(args=None, namespace=None):
             f"total threads (--nthreads/--n_cpus={config.nipype.nprocs})"
         )
 
-    if config.workflow.recon_spec and not config.execution.recon_input:
-        build_log.info("Running BOTH preprocessing and recon.")
-        config.execution.running_preproc_and_recon = True
-        config.execution.recon_input = config.execution.qsiprep_dir
-
     # Validate the tricky options here
     if config.workflow.dwi_denoise_window != "auto":
         try:
@@ -705,9 +697,6 @@ def parse_args(args=None, namespace=None):
     if config.execution.qsiprep_dir is None:
         config.execution.qsiprep_dir = output_dir / "qsiprep"
 
-    if config.execution.qsirecon_dir is None:
-        config.execution.qsirecon_dir = output_dir / "qsirecon"
-
     if config.execution.reportlets_dir is None:
         config.execution.reportlets_dir = work_dir / "reportlets"
 
@@ -735,20 +724,17 @@ def parse_args(args=None, namespace=None):
 
     # Validate inputs
     if not opts.skip_bids_validation:
-        if opts.recon_input is not None:
-            build_log.info("Skipping BIDS validation because inputs are BIDS derivatives")
-        else:
-            from ..utils.bids import validate_input_dir
+        from ..utils.bids import validate_input_dir
 
-            build_log.info(
-                "Making sure the input data is BIDS compliant (warnings can be ignored in most "
-                "cases)."
-            )
-            validate_input_dir(
-                config.environment.exec_env,
-                opts.bids_dir,
-                opts.participant_label,
-            )
+        build_log.info(
+            "Making sure the input data is BIDS compliant (warnings can be ignored in most "
+            "cases)."
+        )
+        validate_input_dir(
+            config.environment.exec_env,
+            opts.bids_dir,
+            opts.participant_label,
+        )
 
     # Setup directories
     config.execution.log_dir = config.execution.qsiprep_dir / "logs"