diff --git a/README.md b/README.md index 50f1e2f..1ed7e69 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,5 @@ [![Documentation Status](https://readthedocs.org/projects/tractoflow-documentation/badge/?version=latest)](https://tractoflow-documentation.readthedocs.io/en/latest/?badge=latest) -# TractoFlow-documentation \ No newline at end of file +# TractoFlow-documentation + +https://tractoflow-documentation.readthedocs.io/en/latest/ diff --git a/source/data/install.sh b/source/data/install.sh index 60fa30e..aa91f8f 100644 --- a/source/data/install.sh +++ b/source/data/install.sh @@ -4,5 +4,5 @@ echo "Downloading TractoFlow..." nextflow pull scilus/tractoflow echo "Done: TractoFlow downloaded." echo "Downloading TractoFlow Singularity..." -wget -q --show-progress http://scil.usherbrooke.ca/containers_list/scilus_1.4.0.sif +wget -q --show-progress http://scil.usherbrooke.ca/containers_list/scilus_1.4.2.sif echo "Done: TractoFlow Singularity downloaded." diff --git a/source/index.rst b/source/index.rst index 224cbc9..e47b5ec 100644 --- a/source/index.rst +++ b/source/index.rst @@ -2,7 +2,7 @@ Welcome to the TractoFlow user documentation! ============================================= .. note:: - New release available: 2.4.0. + New release available: 2.4.1. TractoFlow pipeline is developed by the Sherbrooke Connectivity Imaging Lab (`SCIL`_) in order to process diffusion MRI dataset from the raw data to the tractography. diff --git a/source/installation/install.rst b/source/installation/install.rst index 47ff4c6..e62141f 100644 --- a/source/installation/install.rst +++ b/source/installation/install.rst @@ -7,7 +7,7 @@ Easy install method Enter this command in your terminal (it downloads the container and TractoFlow code in the current directory - Make sure nextflow is already installed before running this command): :: - curl -s https://tractoflow-documentation.readthedocs.io/en/2.4.0/install.sh | bash + curl -s https://tractoflow-documentation.readthedocs.io/en/2.4.1/install.sh | bash Detailed Installation @@ -56,13 +56,13 @@ Download the last release of the Singularity container for TractoFlow: :: - $> wget http://scil.usherbrooke.ca/containers_list/scilus_1.4.0.sif + $> wget http://scil.usherbrooke.ca/containers_list/scilus_1.4.2.sif Or if you have sudo privileges :: - $> sudo singularity build scilus_1.4.0.sif docker://scilus/scilus:1.4.0 + $> sudo singularity build scilus_1.4.2.sif docker://scilus/scilus:1.4.2 For developers ############## @@ -81,7 +81,7 @@ Then, you can build the singularity image: :: - $> singularity build scilus_1.4.0.sif singularity_scilus.def + $> singularity build scilus_1.4.2.sif singularity_scilus.def .. _docker-tractoflow: @@ -95,6 +95,6 @@ Download the last release of the Docker container for TractoFlow: :: - $> docker pull scilus/scilus:1.4.0 + $> docker pull scilus/scilus:1.4.2 Please see :ref:`profiles` section to use `macos` profile. diff --git a/source/pipeline/input.rst b/source/pipeline/input.rst index 1d414e1..bd62cb8 100644 --- a/source/pipeline/input.rst +++ b/source/pipeline/input.rst @@ -6,11 +6,14 @@ Two types of input are available in TractoFlow: BIDS and an in-house structure. BIDS parameter -------------- -We recommend to use ``dcm2bids`` (https://github.com/unfmontreal/Dcm2Bids) to create BIDS datasets. +We recommend to use ``dcm2bids`` (https://github.com/unfmontreal/Dcm2Bids) or ``heuviconv`` (https://github.com/nipy/heudiconv) to create BIDS datasets. TractoFlow supports BIDS as input data using ``--bids YOUR_BIDS_DATASET``. TractoFlow does some verifications before launching the processing to valide the BIDS format. +If you need to filter some subjects/sessions/runs or some files +you can create a bidsignore file using ``--bidsignore bids_ignore_path``. (Check: https://github.com/bids-standard/bids-validator#bidsignore) + In the case that some tags or informations are missing, TractoFlow will create a json file in ``results/Read_BIDS``. Please complete missing informations and relaunch the pipeline replacing ``--bids YOUR_BIDS_DATASET`` with ``--bids_config results/Read_BIDS/tractoflow_bids_struct.json``. diff --git a/source/pipeline/launch.rst b/source/pipeline/launch.rst index f2a612d..358003c 100644 --- a/source/pipeline/launch.rst +++ b/source/pipeline/launch.rst @@ -9,14 +9,14 @@ To run the pipeline, use the following command: :: # With Singularity - $> nextflow run tractoflow -r 2.4.0 --bids input_bids -with-singularity scilus_1.4.0.sif -resume + $> nextflow run tractoflow -r 2.4.1 --bids input_bids -with-singularity scilus_1.4.2.sif -resume # Or - $> nextflow run tractoflow -r 2.4.0 --input input_folder -with-singularity scilus_1.4.0.sif -resume + $> nextflow run tractoflow -r 2.4.1 --input input_folder -with-singularity scilus_1.4.2.sif -resume # With Docker - $> nextflow run tractoflow -r 2.4.0 --bids input_bids -with-docker scilus/scilus:1.4.0 -resume + $> nextflow run tractoflow -r 2.4.1 --bids input_bids -with-docker scilus/scilus:1.4.2 -resume # Or - $> nextflow run tractoflow -r 2.4.0 --input input_folder -with-docker scilus/scilus:1.4.0 -resume + $> nextflow run tractoflow -r 2.4.1 --input input_folder -with-docker scilus/scilus:1.4.2 -resume If you want to skip steps already processed by an anterior run, you can add `-resume` option in the command line. @@ -38,7 +38,7 @@ to be executed with ``sbatch``. #SBATCH --mem=0 #SBATCH --time=48:00:00 - nextflow -c singularity.conf run tractoflow -r 2.4.0 --input input_folder --dti_shells "DTI_SHELLS" --fodf_shells "FODF_SHELLS" -with-singularity singularity_name.sif -resume + nextflow -c singularity.conf run tractoflow -r 2.4.1 --input input_folder --dti_shells "DTI_SHELLS" --fodf_shells "FODF_SHELLS" -with-singularity singularity_name.sif -resume To launch on multiple nodes, you must to use the MPI option that use Ignite executor. The following example use 2 nodes with 32 threads on each nodes. The follwing lines @@ -55,7 +55,7 @@ must be saved in ``.sh`` file (e.g. ``cmd.sh``) to be executed with ``sbatch``. export NXF_CLUSTER_SEED=$(shuf -i 0-16777216 -n 1) - srun nextflow -c singularity.conf run tractoflow -r 2.4.0 --input input_folder --dti_shells "DTI_SHELLS" --fodf_shells "FODF_SHELLS" -with-singularity singularity_name.sif -with-mpi -resume + srun nextflow -c singularity.conf run tractoflow -r 2.4.1 --input input_folder --dti_shells "DTI_SHELLS" --fodf_shells "FODF_SHELLS" -with-singularity singularity_name.sif -with-mpi -resume To launch the pipeline on the HPC: diff --git a/source/pipeline/options.rst b/source/pipeline/options.rst index 608e222..f20e08b 100644 --- a/source/pipeline/options.rst +++ b/source/pipeline/options.rst @@ -2,16 +2,14 @@ Options ======= To display the options of Tractoflow, please use -``nextflow run tractoflow -r 2.4.0 --help``. +``nextflow run tractoflow -r 2.4.1 --help``. Optional BIDS arguments ------------ -``--participants_label "SUBID1 SUBID2"`` (default: none) - The label(s) of the specific participant(s) you want to analyzed. - It does not include "sub-". - Please write one or more subjects between quotes e.g. (--participants_label "01 02 04") - If this parameter is not provided all subjects should be analyzed +``--bidsignore "bids_ignore_path"`` (default: none) + If you want to ignore some subjects/sessions/runs or some files, you can provide an extra bidsignore file. + Check: https://github.com/bids-standard/bids-validator#bidsignore ``-clean_bids BOOL`` (default: false) diff --git a/source/pipeline/profiles.rst b/source/pipeline/profiles.rst index 1d79fb3..c39960f 100644 --- a/source/pipeline/profiles.rst +++ b/source/pipeline/profiles.rst @@ -7,7 +7,7 @@ To select one or multiple profiles, please use the ``-profile`` option. For exam :: - $> nextflow run tractoflow -r 2.4.0 --input input_folder -profile macos,fully_reproducible -with-singularity singularity_name.sif -resume + $> nextflow run tractoflow -r 2.4.1 --input input_folder -profile macos,fully_reproducible -with-singularity singularity_name.sif -resume Profiles available ------------------ diff --git a/source/reference/changelog.rst b/source/reference/changelog.rst index 86acf7f..ad14508 100644 --- a/source/reference/changelog.rst +++ b/source/reference/changelog.rst @@ -1,7 +1,7 @@ Changelog ========= -2.4.0 +2.4.1 ######## Date: November 2022