Rename QSIPrep to QSIRecon (#1)

* pennbbl --> pennlinc

* qsiprep --> qsirecon

* master --> main

* Rename file.

.circleci/config.yml

@@ -3,7 +3,7 @@ version: 2.1
 build: &build
   docker:
     - image: cimg/base:2020.09
-  working_directory: /tmp/src/qsiprep_build
+  working_directory: /tmp/src/qsirecon_build
   steps:
     - checkout
     - setup_remote_docker:
@@ -43,90 +43,90 @@ build: &build
             --rm=false \
             -f ${BUILD_FILE} \
             --build-arg TAG_ANTS=${TAG_ANTS} \
-            -t pennbbl/${IMG_NAME}:${CIRCLE_TAG} .
+            -t pennlinc/${IMG_NAME}:${CIRCLE_TAG} .
 
           if [[ -n "$DOCKER_PASS" ]]; then
             docker login -u $DOCKER_USER -p $DOCKER_PASS
-            docker push pennbbl/${IMG_NAME}:$CIRCLE_TAG
+            docker push pennlinc/${IMG_NAME}:$CIRCLE_TAG
           fi
 
 jobs:
 
   build_FSL:
     environment:
       VERSION_TAG: "TAG_FSL"
-      IMG_NAME: "qsiprep-fsl"
+      IMG_NAME: "qsirecon-fsl"
       BUILD_FILE: "Dockerfile_FSLconda"
     <<: *build
 
   build_FreeSurfer:
     environment:
       VERSION_TAG: "TAG_FREESURFER"
-      IMG_NAME: "qsiprep-freesurfer"
+      IMG_NAME: "qsirecon-freesurfer"
       BUILD_FILE: "Dockerfile_FreeSurfer"
     <<: *build
 
   build_3Tissue:
     environment:
       VERSION_TAG: "TAG_3TISSUE"
-      IMG_NAME: "qsiprep-3tissue"
+      IMG_NAME: "qsirecon-3tissue"
       BUILD_FILE: "Dockerfile_3Tissue"
     <<: *build
 
   build_MRtrix3:
     environment:
       VERSION_TAG: "TAG_MRTRIX3"
-      IMG_NAME: "qsiprep-mrtrix3"
+      IMG_NAME: "qsirecon-mrtrix3"
       BUILD_FILE: "Dockerfile_MRtrix3"
     <<: *build
 
   build_AFNI:
     environment:
       VERSION_TAG: "TAG_AFNI"
-      IMG_NAME: "qsiprep-afni"
+      IMG_NAME: "qsirecon-afni"
       BUILD_FILE: "Dockerfile_AFNI"
     <<: *build
 
   build_DSIStudio:
     environment:
       VERSION_TAG: "TAG_DSISTUDIO"
-      IMG_NAME: "qsiprep-dsistudio"
+      IMG_NAME: "qsirecon-dsistudio"
       BUILD_FILE: "Dockerfile_DSIStudio"
     <<: *build
 
   build_ANTs:
     environment:
       VERSION_TAG: "TAG_ANTS"
-      IMG_NAME: "qsiprep-ants"
+      IMG_NAME: "qsirecon-ants"
       BUILD_FILE: "Dockerfile_ANTs"
     resource_class: large
     <<: *build
 
   build_Miniconda:
     environment:
       VERSION_TAG: "TAG_MINICONDA"
-      IMG_NAME: "qsiprep-miniconda"
+      IMG_NAME: "qsirecon-miniconda"
       BUILD_FILE: "Dockerfile_Miniconda"
     <<: *build
 
   build_Micromamba:
     environment:
       VERSION_TAG: "TAG_MICROMAMBA"
-      IMG_NAME: "qsiprep-micromamba"
+      IMG_NAME: "qsirecon-micromamba"
       BUILD_FILE: "Dockerfile_Micromamba"
     <<: *build
 
   build_TORTOISE:
     environment:
       VERSION_TAG: "TAG_TORTOISE"
-      IMG_NAME: "qsiprep-drbuddi"
+      IMG_NAME: "qsirecon-drbuddi"
       BUILD_FILE: "Dockerfile_TORTOISE"
     <<: *build
 
   build_TORTOISECUDA:
     environment:
       VERSION_TAG: "TAG_TORTOISECUDA"
-      IMG_NAME: "qsiprep-drbuddicuda"
+      IMG_NAME: "qsirecon-drbuddicuda"
       BUILD_FILE: "Dockerfile_TORTOISEcuda"
     <<: *build
 
@@ -135,7 +135,7 @@ jobs:
       TZ: "/usr/share/zoneinfo/America/New_York"
     docker:
       - image: cimg/base:2020.09
-    working_directory: /tmp/src/qsiprep_build
+    working_directory: /tmp/src/qsirecon_build
     steps:
       - checkout
       - setup_remote_docker:
@@ -149,15 +149,15 @@ jobs:
               source setup_build.sh
               do_build build_fsl
               docker login -u $DOCKER_USER -p $DOCKER_PASS
-              docker push pennbbl/qsiprep_build:$CIRCLE_TAG
+              docker push pennlinc/qsirecon_build:$CIRCLE_TAG
             fi
 
   build_nofsl:
     environment:
       TZ: "/usr/share/zoneinfo/America/New_York"
     docker:
       - image: cimg/base:2020.09
-    working_directory: /tmp/src/qsiprep_build
+    working_directory: /tmp/src/qsirecon_build
     steps:
       - checkout
       - setup_remote_docker:
@@ -171,7 +171,7 @@ jobs:
               source setup_build.sh
               do_build no_fsl
               docker login -u $DOCKER_USER -p $DOCKER_PASS
-              docker push pennbbl/qsiprep_build:${CIRCLE_TAG}-nofsl
+              docker push pennlinc/qsirecon_build:${CIRCLE_TAG}-nofsl
             fi
 
   deployable:

Dockerfile

@@ -14,37 +14,37 @@ ARG TAG_TORTOISECUDA
 ARG FSL_BUILD
 
 # COPY can't handle variables, so here we go
-FROM pennbbl/qsiprep-fsl:${TAG_FSL} as build_fsl
-FROM pennbbl/qsiprep-freesurfer:${TAG_FREESURFER} as build_freesurfer
-FROM pennbbl/qsiprep-ants:${TAG_ANTS} as build_ants
-FROM pennbbl/qsiprep-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3
-FROM pennbbl/qsiprep-3tissue:${TAG_3TISSUE} as build_3tissue
-FROM pennbbl/qsiprep-dsistudio:${TAG_DSISTUDIO} as build_dsistudio
-FROM pennbbl/qsiprep-micromamba:${TAG_MICROMAMBA} as build_micromamba
-FROM pennbbl/qsiprep-afni:${TAG_AFNI} as build_afni
-FROM pennbbl/qsiprep-drbuddi:${TAG_TORTOISE} as build_tortoise
-FROM pennbbl/qsiprep-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda
+FROM pennlinc/qsirecon-fsl:${TAG_FSL} as build_fsl
+FROM pennlinc/qsirecon-freesurfer:${TAG_FREESURFER} as build_freesurfer
+FROM pennlinc/qsirecon-ants:${TAG_ANTS} as build_ants
+FROM pennlinc/qsirecon-mrtrix3:${TAG_MRTRIX3} as build_mrtrix3
+FROM pennlinc/qsirecon-3tissue:${TAG_3TISSUE} as build_3tissue
+FROM pennlinc/qsirecon-dsistudio:${TAG_DSISTUDIO} as build_dsistudio
+FROM pennlinc/qsirecon-micromamba:${TAG_MICROMAMBA} as build_micromamba
+FROM pennlinc/qsirecon-afni:${TAG_AFNI} as build_afni
+FROM pennlinc/qsirecon-drbuddi:${TAG_TORTOISE} as build_tortoise
+FROM pennlinc/qsirecon-drbuddicuda:${TAG_TORTOISE} as build_tortoisecuda
 FROM pennlinc/atlaspack:0.1.0 as atlaspack
 FROM nvidia/cuda:11.1.1-runtime-ubuntu18.04 as ubuntu
 
 # Make a dummy fsl image containing no FSL
 FROM ubuntu as no_fsl
-RUN mkdir -p /opt/conda/envs/fslqsiprep/bin \
-    && touch /opt/conda/envs/fslqsiprep/bin/eddy_cuda10.2
+RUN mkdir -p /opt/conda/envs/fslqsirecon/bin \
+    && touch /opt/conda/envs/fslqsirecon/bin/eddy_cuda10.2
 
 FROM ${FSL_BUILD} as this-fsl
 
 FROM ubuntu
 ## FSL
-COPY --from=this-fsl /opt/conda/envs/fslqsiprep /opt/conda/envs/fslqsiprep
-ENV FSLDIR="/opt/conda/envs/fslqsiprep" \
+COPY --from=this-fsl /opt/conda/envs/fslqsirecon /opt/conda/envs/fslqsirecon
+ENV FSLDIR="/opt/conda/envs/fslqsirecon" \
     FSLOUTPUTTYPE="NIFTI_GZ" \
     FSLMULTIFILEQUIT="TRUE" \
     FSLLOCKDIR="" \
     FSLMACHINELIST="" \
     FSLREMOTECALL="" \
     FSLGECUDAQ="cuda.q" \
-    PATH="/opt/conda/envs/fslqsiprep/bin:$PATH" \
+    PATH="/opt/conda/envs/fslqsirecon/bin:$PATH" \
     FSL_DEPS="libquadmath0" \
     FSL_BUILD="${FSL_BUILD}"
 
@@ -73,7 +73,7 @@ ENV PATH="$PATH:/opt/mrtrix3-latest/bin:/opt/3Tissue/bin" \
 ## Freesurfer
 COPY --from=build_freesurfer /opt/freesurfer /opt/freesurfer
 # Simulate SetUpFreeSurfer.sh
-ENV FSL_DIR="/opt/conda/envs/fslqsiprep" \
+ENV FSL_DIR="/opt/conda/envs/fslqsirecon" \
     OS="Linux" \
     FS_OVERRIDE=0 \
     FIX_VERTEX_AREA="" \
@@ -107,13 +107,13 @@ ENV PATH="$PATH:/src/TORTOISEV4/bin" \
     TORTOISE_DEPS="fftw3"
 
     # Create a shared $HOME directory
-RUN useradd -m -s /bin/bash -G users qsiprep
-WORKDIR /home/qsiprep
+RUN useradd -m -s /bin/bash -G users qsirecon
+WORKDIR /home/qsirecon
 
 ## Python, compiled dependencies
-COPY --from=build_micromamba /opt/conda/envs/qsiprep /opt/conda/envs/qsiprep
-COPY --from=build_micromamba /home/qsiprep/.dipy /home/qsiprep/.dipy
-ENV PATH="/opt/conda/envs/qsiprep/bin:$PATH"
+COPY --from=build_micromamba /opt/conda/envs/qsirecon /opt/conda/envs/qsirecon
+COPY --from=build_micromamba /home/qsirecon/.dipy /home/qsirecon/.dipy
+ENV PATH="/opt/conda/envs/qsirecon/bin:$PATH"
 
 RUN apt-get update -qq \
     && apt-get install -y -q --no-install-recommends \
@@ -211,20 +211,20 @@ RUN cd /opt/art \
 # Unless otherwise specified each process should only use one thread - nipype
 # will handle parallelization
 ENV \
-    HOME="/home/qsiprep" \
+    HOME="/home/qsirecon" \
     MKL_NUM_THREADS=1 \
     OMP_NUM_THREADS=1 \
     MRTRIX_NTHREADS=1 \
     KMP_WARNINGS=0 \
     CRN_SHARED_DATA=/niworkflows_data \
     IS_DOCKER_8395080871=1 \
     ARTHOME="/opt/art" \
-    DIPY_HOME=/home/qsiprep/.dipy \
+    DIPY_HOME=/home/qsirecon/.dipy \
     QTDIR=$QT_BASE_DIR \
     PATH=$QT_BASE_DIR/bin:$PATH \
     LD_LIBRARY_PATH=$QT_BASE_DIR/lib/x86_64-linux-gnu:$QT_BASE_DIR/lib:$LD_LIBRARY_PATH \
     PKG_CONFIG_PATH=$QT_BASE_DIR/lib/pkgconfig:$PKG_CONFIG_PATH \
-    LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nvidia/cudnn/lib
+    LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/conda/envs/qsirecon/lib/python3.10/site-packages/nvidia/cudnn/lib
 
 WORKDIR /root/
 
@@ -258,7 +258,7 @@ RUN pyAFQ download
 
 # Make singularity mount directories
 RUN  mkdir -p /sngl/data \
-  && mkdir /sngl/qsiprep-output \
+  && mkdir /sngl/qsirecon-output \
   && mkdir /sngl/out \
   && mkdir /sngl/scratch \
   && mkdir /sngl/spec \

Dockerfile_ANTs

@@ -93,7 +93,7 @@ FROM base
 COPY --from=builder /opt/ants /opt/ants
 COPY --from=builder /tmp/ants /tmp/ants
 
-LABEL maintainer="ANTsX team: Forked by QSIPrep team" \
+LABEL maintainer="ANTsX team: Forked by QSIRecon team" \
       description="ANTs is part of the ANTsX ecosystem (https://github.com/ANTsX). \
 ANTs Citation: https://pubmed.ncbi.nlm.nih.gov/24879923"
 

Dockerfile_Micromamba

@@ -35,12 +35,12 @@ RUN apt-get update && \
                     libglu1-mesa-dev \
                     bzip2 \
                     libgomp1 \
-                    wget 
+                    wget
 
 # Create a shared $HOME directory
-RUN useradd -m -s /bin/bash -G users qsiprep
-WORKDIR /home/qsiprep
-ENV HOME="/home/qsiprep"
+RUN useradd -m -s /bin/bash -G users qsirecon
+WORKDIR /home/qsirecon
+ENV HOME="/home/qsirecon"
 
 
 WORKDIR /
@@ -51,12 +51,12 @@ ENV MAMBA_ROOT_PREFIX="/opt/conda" \
     MAMBA_NO_LOW_SPEED_LIMIT=1 \
     PIP_DEFAULT_TIMEOUT=100
 
-COPY qsiprep_env.yml /tmp/env.yml
+COPY qsirecon_env.yml /tmp/env.yml
 
 WORKDIR /tmp
 RUN micromamba config set extract_threads 1
 RUN micromamba create -vv -y -f /tmp/env.yml
-ENV PATH=/opt/conda/envs/qsiprep/bin:$PATH
+ENV PATH=/opt/conda/envs/qsirecon/bin:$PATH
 RUN micromamba clean -y -a
 
 RUN \

Dockerfile_TORTOISE

@@ -1,6 +1,6 @@
 ARG TAG_ANTS
 
-FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base
+FROM pennlinc/qsirecon-ants:${TAG_ANTS} as base
 FROM base as builder
 RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
 
@@ -45,7 +45,7 @@ RUN \
       -DCMAKE_C_COMPILER=/usr/bin/gcc-9 \
       -DCMAKE_CXX_COMPILER=/usr/bin/g++-9 \
       -DUSECUDA=0 \
-      -DQSIPREP=1 \
+      -DQSIRECON=1 \
       -DITK_DIR=/tmp/ants/build/ITKv5-build \
       -DISDEBUG=0 \
       && \

Dockerfile_TORTOISEcuda

@@ -1,6 +1,6 @@
 ARG TAG_ANTS
 
-FROM pennbbl/qsiprep-ants:${TAG_ANTS} as base
+FROM pennlinc/qsirecon-ants:${TAG_ANTS} as base
 FROM base as builder
 RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
 
@@ -45,7 +45,7 @@ RUN \
       -DCMAKE_C_COMPILER=/usr/bin/gcc-9 \
       -DCMAKE_CXX_COMPILER=/usr/bin/g++-9 \
       -DUSECUDA=1 \
-      -DQSIPREP=1 \
+      -DQSIRECON=1 \
       -DITK_DIR=/tmp/ants/build/ITKv5-build \
       -DISDEBUG=0 \
       && \

README.rst

@@ -1,22 +1,22 @@
 .. include:: links.rst
 
-QSIprep: Preprocessing and analysis of q-space images
+QSIRecon: Reconstruction of preprocessed q-space images
 =======================================================
 
-.. image:: https://readthedocs.org/projects/qsiprep/badge/?version=latest
-  :target: http://qsiprep.readthedocs.io/en/latest/?badge=latest
+.. image:: https://readthedocs.org/projects/qsirecon/badge/?version=latest
+  :target: http://qsirecon.readthedocs.io/en/latest/?badge=latest
   :alt: Documentation Status
 
-.. image:: https://circleci.com/gh/PennLINC/qsiprep/tree/master.svg?style=svg
-  :target: https://circleci.com/gh/PennLINC/qsiprep/tree/master
+.. image:: https://circleci.com/gh/PennLINC/qsirecon/tree/main.svg?style=svg
+  :target: https://circleci.com/gh/PennLINC/qsirecon/tree/main
 
 
-Full documentation at https://qsiprep.readthedocs.io
+Full documentation at https://qsirecon.readthedocs.io
 
 About
 -----
 
-``qsiprep`` configures pipelines for processing diffusion-weighted MRI (dMRI) data.
+``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.
@@ -27,7 +27,7 @@ The main features of this software are
      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/PennBBL/qsiprep/raw/master/docs/_static/workflow_full.png
+.. image:: https://github.com/PennLINC/qsirecon/raw/main/docs/_static/workflow_full.png
 
 
 .. _preprocessing_def:
@@ -47,7 +47,7 @@ Reconstruction
 ~~~~~~~~~~~~~~~~
 
 The outputs from the :ref:`preprocessing_def` pipelines can be reconstructed in many other
-software packages. We provide a curated set of :ref:`recon_workflows` in ``qsiprep``
+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.
 
@@ -56,6 +56,6 @@ connectivity.
 Note
 ------
 
-The ``qsiprep`` pipeline uses much of the code from ``FMRIPREP``. It is critical
+The ``qsirecon`` pipeline uses much of the code from ``FMRIPREP``. It is critical
 to note that the similarities in the code **do not imply that the authors of
 FMRIPREP in any way endorse or support this code or its pipelines**.