Start removing QSIPrep-specific code and documentation (#4)

* Move qsirecon workflow. * Fix imports. * Update CHANGES and README. * Drop exec_mode. * Change some preprocessing to reconstruction.
PennLINC · Aug 9, 2024 · d071473 · d071473
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diff --git a/.zenodo.json b/.zenodo.json
@@ -74,7 +74,7 @@
     "dMRI",
     "BIDS"
   ],
-  "title": "QSIRecon: An integrative platform for preprocessing and reconstructing diffusion MRI",
+  "title": "QSIRecon: An integrative platform for reconstructing diffusion MRI",
   "license": "BSD-3-Clause",
   "upload_type": "software"
 }
diff --git a/CHANGES.rst b/CHANGES.rst
diff --git a/Dockerfile b/Dockerfile
@@ -26,7 +26,7 @@ ARG VCS_REF
 ARG VERSION
 LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.name="qsirecon" \
-      org.label-schema.description="qsirecon - q Space Images preprocessing tool" \
+      org.label-schema.description="qsirecon - q Space Images postprocessing tool" \
       org.label-schema.url="http://qsirecon.readthedocs.io" \
       org.label-schema.vcs-ref=$VCS_REF \
       org.label-schema.vcs-url="https://github.com/pennlinc/qsirecon" \

diff --git a/README.rst b/README.rst
@@ -1,6 +1,6 @@
 .. include:: links.rst
 
-QSIRecon: Preprocessing and analysis of q-space images
+QSIRecon: Reconstruction of preprocessed q-space images
 =======================================================
 
 .. image:: https://img.shields.io/badge/Source%20Code-pennlinc%2Fqsirecon-purple
@@ -36,34 +36,18 @@ About
 ``qsirecon`` configures pipelines for processing diffusion-weighted MRI (dMRI) data.
 The main features of this software are
 
-  1. A BIDS-app approach to preprocessing nearly all kinds of modern diffusion MRI data.
-  2. Automatically generated preprocessing pipelines that correctly group, distortion correct,
-     motion correct, denoise, coregister and resample your scans, producing visual reports and
-     QC metrics.
-  3. A system for running state-of-the-art reconstruction pipelines that include algorithms
+  1. A system for running state-of-the-art reconstruction pipelines that include algorithms
      from Dipy_, MRTrix_, `DSI Studio`_  and others.
-  4. A novel motion correction algorithm that works on DSI and random q-space sampling schemes
 
 .. image:: https://github.com/PennLINC/qsirecon/raw/main/docs/_static/workflow_full.png
 
 
-.. _preprocessing_def:
-
-Preprocessing
-~~~~~~~~~~~~~~~
-
-The preprocessing pipelines are built based on the available BIDS inputs, ensuring that fieldmaps
-are handled correctly. The preprocessing workflow performs head motion correction, susceptibility
-distortion correction, MP-PCA denoising, coregistration to T1w images, spatial normalization
-using ANTs_ and tissue segmentation.
-
-
 .. _reconstruction_def:
 
 Reconstruction
 ~~~~~~~~~~~~~~~~
 
-The outputs from the :ref:`preprocessing_def` pipelines can be reconstructed in many other
+The outputs from BIDS-compliant preprocessing pipelines can be reconstructed in many other
 software packages. We provide a curated set of :ref:`recon_workflows` in ``qsirecon``
 that can run ODF/FOD reconstruction, tractography, Fixel estimation and regional
 connectivity.

diff --git a/docs/api.rst b/docs/api.rst
@@ -16,24 +16,14 @@ Internal configuration system
 Library API
 ***********
 
-Preprocessing Workflows
------------------------
-
-.. toctree::
-   :glob:
-
-   api/qsirecon.workflows.base
-   api/qsirecon.workflows.anatomical
-   api/qsirecon.workflows.dwi
-   api/qsirecon.workflows.fieldmap
-
 
 Reconstruction Workflows
 ------------------------
 
 .. toctree::
    :glob:
 
+   api/qsirecon.workflows.base
    api/qsirecon.workflows.recon
 
 

diff --git a/docs/citing.rst b/docs/citing.rst
@@ -5,7 +5,7 @@
 ===============
 Citing qsirecon
 ===============
-.. [Cieslak2022] Cieslak, M., Cook, P.A., He, X. et al. (2021) QSIRecon: an integrative platform for preprocessing and reconstructing diffusion MRI data.     Nat Methods 18 (775–778) doi: https://doi.org/10.1038/s41592-021-01185-5
+.. [Cieslak2022] Cieslak, M., Cook, P.A., He, X. et al. (2021) QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data.     Nat Methods 18 (775–778) doi: https://doi.org/10.1038/s41592-021-01185-5
 
 .. [Fonov2011] Fonov VS, Evans AC, Botteron K, Almli CR, McKinstry RC, Collins DL and BDCG,
     Unbiased average age-appropriate atlases for pediatric studies, NeuroImage 54(1), 2011

diff --git a/docs/comparisons.md b/docs/comparisons.md
@@ -21,7 +21,7 @@ their current feature sets. These other
 
 ## Preprocessing
 
-|                                                     | QSIRecon                  | Tractoflow             | PreQual                 | MRtrix3_connectome | dMRIPrep         |
+|                                                     | QSIPrep                  | Tractoflow             | PreQual                 | MRtrix3_connectome | dMRIPrep         |
 | --------------------------------------------------- | :----------------------: | :--------------------: | :---------------------: | :----------------: | :--------------: |
 | BIDS App                                            |            ✔             |           ✔            |            ✘            |         ✔          |        ✔         |
 | Gradient direction sanity check                     |     Q-form matching      |           ✘            |     `dwigradcheck`      |         ✘          |        ✘         |

diff --git a/docs/index.rst b/docs/index.rst
@@ -15,7 +15,6 @@ Contents
    installation
    quickstart
    usage
-   preprocessing
    reconstruction
    contributors
    citing