Merge pull request #18 from scilus/update_doc_with_fs_and_bidsignore

Add bidsignore doc

Author: arnaudbore

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
+# TractoFlow-documentation
+
+https://tractoflow-documentation.readthedocs.io/en/latest/

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."

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.

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.

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``.
 

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:
 

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)

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
 ------------------

source/reference/changelog.rst

@@ -1,7 +1,7 @@
 Changelog
 =========
 
-2.4.0
+2.4.1
 ########
 Date: November 2022