Merge pull request #12 from arnaudbore/update_release_2.2.1

Update to tractoflow 2.2.1

source/conf.py

@@ -20,7 +20,7 @@
 # -- Project information -----------------------------------------------------
 
 project = u'TractoFlow-documentation'
-copyright = u'2019, SCIL'
+copyright = u'2021, SCIL'
 author = u'SCIL'
 
 # The short X.Y version

source/data/install.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 
 echo "Downloading TractoFlow..."
-wget -q https://github.com/scilus/tractoflow/releases/download/2.1.1/tractoflow-2.1.1.zip
-unzip -q tractoflow-2.1.1.zip
-rm -rf tractoflow-2.1.1.zip
+wget -q https://github.com/scilus/tractoflow/releases/download/2.2.1/tractoflow-2.2.1.zip
+unzip -q tractoflow-2.2.1.zip
+rm -rf tractoflow-2.2.1.zip
 echo "Done: TractoFlow downloaded."
 echo "Downloading TractoFlow Singularity..."
-wget -q --show-progress http://scil.dinf.usherbrooke.ca/containers_list/tractoflow_2.1.1_650f776_2020-07-15.img
+wget -q --show-progress http://scil.dinf.usherbrooke.ca/containers_list/tractoflow_2.2.1_b9a527_2021-04-13.sif
 echo "Done: TractoFlow Singularity downloaded."

source/index.rst

@@ -2,7 +2,7 @@ Welcome to the TractoFlow user documentation!
 =============================================
 
 .. note::
-    New release available: 2.1.1.
+    New release available: 2.2.1.
     TractoFlow now support BIDS as input data.
 
 TractoFlow pipeline is developed by the Sherbrooke Connectivity Imaging Lab (`SCIL`_)

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):
 ::
 
-    curl -s https://tractoflow-documentation.readthedocs.io/en/2.1.1/install.sh | bash
+    curl -s https://tractoflow-documentation.readthedocs.io/en/2.2.1/install.sh | bash
 
 TractoFlow pipeline
 -------------------
@@ -19,7 +19,7 @@ Download the last release of TractoFlow pipeline:
 
 ::
 
-    $> wget https://github.com/scilus/tractoflow/releases/download/2.1.1/tractoflow-2.1.1.zip && unzip tractoflow-2.1.1.zip
+    $> wget https://github.com/scilus/tractoflow/releases/download/2.2.1/tractoflow-2.2.1.zip && unzip tractoflow-2.2.1.zip
 
 For developers
 ##############
@@ -47,7 +47,7 @@ Download the last release of the Singularity container for TractoFlow:
 
 ::
 
-    $> wget http://scil.dinf.usherbrooke.ca/containers_list/tractoflow_2.1.1_650f776_2020-07-15.img
+    $> wget http://scil.dinf.usherbrooke.ca/containers_list/tractoflow_2.2.1_b9a527_2021-04-13.sif
 
 For developers
 ##############
@@ -80,6 +80,6 @@ Download the last release of the Docker container for TractoFlow:
 
 ::
 
-    $> docker pull scilus/docker-tractoflow:2.1.1
+    $> docker pull scilus/tractoflow:2.2.1
 
 Please see :ref:`profiles` section to use `macos` profile.

source/installation/requirements.rst

@@ -23,7 +23,7 @@ Local Computer
 High Performance computer (HPC)
 ###############################
 
-1. Try ``module load java/1.8.0_121`` or check with your administrator or on the HPC website.
+1. Try ```module load nixpkgs/16.09 module load java/1.8.0_192`` or check with your administrator or on the HPC website.
 2. Use ``wget`` to install Nextflow, change the name, add execution rights and add the Nextflow path in the bash_profile.
 
 ::
@@ -74,4 +74,3 @@ Windows
 To install Docker on your Windows computer, please check the following link:
 
 https://hub.docker.com/editions/community/docker-ce-desktop-windows
-

source/pipeline/input.rst

@@ -6,7 +6,7 @@ Two types of input are available in TractoFlow: BIDS and an in-house structure.
 BIDS parameter
 --------------
 
-We recommend to use ``dcm2bids`` (https://github.com/cbedetti/Dcm2Bids) to create BIDS datasets.
+We recommend to use ``dcm2bids`` (https://github.com/unfmontreal/Dcm2Bids) 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.

source/pipeline/options.rst

@@ -4,6 +4,20 @@ Options
 To display the options of Tractoflow, please use
 ``nextflow run tractoflow/main.nf --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
+
+
+``-clean_bids BOOL`` (default: false)
+  If set, it will remove all the participants that are missing any information.
+
+
 Options list
 ------------
 ``--b0_thr_extract_b0 MAX_VALUE``  (default: 10)
@@ -134,47 +148,97 @@ Options list
     Minimal threshold of MD in mm^2/s to be considered as ventricule voxel.
     Used to compute the ventricules mask and find the maximum fODF amplitude in the ventricules.
 
-``--wm_seeding BOOL`` (default: true)
-    If '--wm_seeding true', use the WM-GM interface and the WM mask as seeding mask,
-    else use the WM-GM interface as seeding mask.
 
-``--algo ALGO`` (default: prob)
-    Tracking algorithm [prob, det].
+Optional PFT Tracking arguments
+------------
+
+``--run_pft_tracking BOOL`` (default: true).
+    [PFT] Run Particle Filter Tracking (PFT)
+
+``--pft_seeding_mask_type TYPE`` (default: wm)
+    [PFT] Seeding mask type [wm, interface, fa].
+
+``--pft_fa_seeding_mask_threshold THRESHOLD`` (default: 0.1)
+    [PFT] FA threshold for FA seeding mask.
+
+``--pft_algo ALGO`` (default: prob)
+    [PFT] Tracking algorithm [prob, det].
+
+``--pft_seeding SEEDING`` (default: npv)
+    [PFT] Seeding type [npv, nt].
+
+``--pft_nbr_seeds NBRSEEDS``  (default: 10)
+    [PFT] Number of seeds related to the seeding type param.
+
+``--pft_step SIZE`` (default: 0.5)
+    [PFT] Step size.
+
+``--pft_theta ANGLE`` (default: 20)
+    [PFT] Maximum angle between 2 steps.
+
+``--pft_min_len LENGTH`` (default: 20)
+    [PFT] Minimum length.
+
+``--pft_max_len LENGTH`` (default: 200)
+    [PFT] Maximum length.
+
+``--pft_compress_streamlines BOOL`` (default: true)
+    [PFT] Compress streamlines.
+
+``--pft_compress_value THRESHOLD`` (default: 0.2)
+    [PFT] Compression error threshold.
+    See [Presseau et al Neuroimage 2015] and [Rheault et al Front Neuroinform 2017].
+
+``--pft_random_seed RANDOMSEED`` (default: 0)
+    [PFT] List of random seed numbers for the random number generator.
+    Please write them as list separated using commat WITHOUT SPACE e.g. (--pft_random_seed 0,1,2)
+
+
+Optional Local Tracking arguments
+------------
+
+``--run_local_tracking BOOL`` (default: false).
+    [LOCAL] Run Local Tracking
+
+``--local_seeding_mask_type TYPE`` (default: wm)
+    [LOCAL] Seeding mask type [wm, interface, fa].
+
+``--local_fa_seeding_mask_threshold THRESHOLD`` (default: 0.1)
+    [LOCAL] FA threshold for FA seeding mask.
+
+``--local_algo ALGO`` (default: prob)
+    [LOCAL] Tracking algorithm [prob, det].
 
-    | prob: streamline probabilistic.
-    | det: streamline deterministic.
+``--local_seeding SEEDING`` (default: npv)
+    [LOCAL] Seeding type [npv, nt].
 
-``--seeding TYPE`` (default: npv)
-    Seeding type [npv, nt].
+``--local_nbr_seeds NBRSEEDS``  (default: 10)
+    [LOCAL] Number of seeds related to the seeding type param.
 
-    | npv: number of seeds per voxel of the seeding mask
-    | nt: total number of seeds randomly placed in the seeding mask
+``--local_step SIZE`` (default: 0.5)
+    [LOCAL] Step size.
 
-``--nbr_seeds NUMBER`` (default: 10)
-    Number of seeds related to the seeding type param.
+``--local_theta ANGLE`` (default: 20)
+    [LOCAL] Maximum angle between 2 steps.
 
-``--random SEED`` (default: 0)
-    Random seed.
-    Fixed for reproducible seeds
+``--local_min_len LENGTH`` (default: 20)
+    [LOCAL] Minimum length.
 
-``--step SIZE`` (default: 0.5)
-    Step size in mm.
+``--local_max_len LENGTH`` (default: 200)
+    [LOCAL] Maximum length.
 
-``--theta ANGLE`` (default: 20)
-    Maximum angle between 2 steps in degrees.
+``--local_compress_streamlines BOOL`` (default: true)
+    [LOCAL] Compress streamlines.
 
-``--min_len LENGTH`` (default: 20)
-    Minimum length in mm.
+``--local_compress_value THRESHOLD`` (default: 0.2)
+    [LOCAL] Compression error threshold.
+    See [Presseau et al Neuroimage 2015] and [Rheault et al Front Neuroinform 2017].
 
-``--max_len LENGTH`` (default: 200)
-    Maximum length in mm.
+``--local_random_seed RANDOMSEED`` (default: 0)
+    [LOCAL] List of random seed numbers for the random number generator.
+    Please write them as list separated using commat WITHOUT SPACE e.g. (--local_random_seed 0,1,2)
 
-``--compress_streamlines BOOL`` (default: true)
-    Compress streamlines.
 
-``--compress_value THRESHOLD`` (default: 0.2)
-    Compression error threshold in mm.
-    See [Presseau et al Neuroimage 2015] and [Rheault et al Front Neuroinform 2017]
 
 ``--template_t1 PATH`` (default: /human-data/mni_152_sym_09c/t1)
     Path to the template T1 directory for antsBrainExtraction.

source/pipeline/profiles.rst

@@ -22,3 +22,6 @@ Profiles available
 ``fully_reproducible``
     When this profile is used, all the parameters will be set to have 100% reproducible results.
     This profile consist to set multi-thread parameters to be fully reproducible [Theaud20].
+
+``cbrain``
+    When this profile is used, Nextflow will copy all the output files in publishDir and not use symlinks.

source/pipeline/steps.rst

@@ -38,4 +38,8 @@ T1 processes
 
 Tractography
 ------------
-The particle filter tractography is performed. Two types of seeding are available: WM-GM interface or WM mask.
+    * Particule Filter Tractography
+    * Local tracking (Optional)
+
+
+The particle filter tractography is performed by default. Three types of seeding are available: WM-GM interface, WM mask or FA.

source/reference/changelog.rst

@@ -1,11 +1,25 @@
 Changelog
 =========
 
+2.2.1
+#########
+Date: 09 April 2021
+
+Bug Fixed:
+  - fully reproducible (ANTS_RANDOM_SEED fixed)
+  - Tracking with FA (typo)
+
+New options:
+  - participants_label: select specific subjects (BIDS input)
+  - clean_bids: remove subject that are not complete (BIDS input)
+
 2.1.1
 #########
 Date: 08 Jul 2020
 
-Support 4D reverse B0 images.
+New features:
+
+  - Support 4D reverse B0 images.
 
 2.1.0
 #########