SCIL software - PaulBautin/tpil_dmri GitHub Wiki

Scilpy is the main library supporting research and development at the Sherbrooke Connectivity Imaging Lab.

git clone https://github.com/scilus/scilpy.git

cd scilpy

pip install -e .

(Installation of scipy requires sudo apt-get install gfortran)

git clone https://github.com/scilus/tractoflow.git in directory scil

git clone https://github.com/scilus/containers-tractoflow.git in directory scil

singularity build tractoflow_2_3_0_container_2_2_1.img singularity_tractoflow.def in new directory containers

Download MI-Brain tarball from Github repository releases then extract with command: tar –xvzf MI-Brain-2020.04.09_r2e0ff5-linux-x86_64.tar.gz

It is now possible to place MI-Brain in HOME directory with command: mv MI-Brain-2020.04.09_r2e0ff5-linux-x86_64 ~/MI-Brain

To accelerate opening add mibrain alias to .bashrc: alias mibrain="bash ~/MI_Brain/MI-Brain.sh"

Quality control can be run with dmriqc_flow github repository

Clone dmriqc_flow github repository with command: git clone https://github.com/scilus/dmriqc_flow.git in scil_dev

To build singularity image run command: sudo singularity build scilus_1.3.0.sif docker://scilus/scilus:1.3.0 in scil_dev/containers

First clone the combine_flows Github repository

When preparing the dataset for reconbundleX use command.

bash tree_for_rbx_flow.sh \
-t <tractoflow/results> \
-o <output_dir>

We have also created a new script for isolating NAC_mPFC bundle. To create the tree run:

bash /home/pabaua/scratch/scil_dev/combine_flows/tree_for_new_bundle.sh \
-r /home/pabaua/scratch/tpil_dev/results/sub-DCL/22-07-11_rbx/results_rbx/ \
-t /home/pabaua/scratch/tpil_dev/results/sub-DCL/22-07-07_tractoflow/results/ \
-a /home/pabaua/scratch/scil_dev/atlas/BN_Atlas_246_1mm.nii.gz \
-o /home/pabaua/scratch/tpil_dev/data/data_new_bundle_DCL

To run tractometry with the output of the new script for isolating NAC_mPFC bundle, run command:

bash /home/pabaua/scratch/tpil_dev/github/tpil_dmri/tree_for_tractometry_p.sh \
-r /home/pabaua/scratch/tpil_dev/results/sub-CON/22-07-12_rbx/results_rbx \
-t /home/pabaua/scratch/tpil_dev/results/sub-CON/22-07-10_tractoflow/results \
-b /home/pabaua/scratch/tpil_dev/results/sub-CON/22-08-16_NAC_mPFC/results_bundle \
-o /home/pabaua/scratch/tpil_dev/data/data_tractometry_with_NACmPFC_CON