How to use

How to use RTP-pipeline

Input files

The input files need to be sorted in independent folders. We recommend that you create a basedir directory and store all subject information there. Inside basedir, create the input and output folders.

mkdir /Users/myusername/testFolder
export basedir=/Users/myusername/testFolder
cd $basedir
mkdir input
mkdir output

Inside the input folder, each file type will have an independent folder name. Below, the explanation of each file type. Important: the folder names need to be exactly the same as below.

If you are using Flywheel, there will be a GUI in the web browser and no need to create a folder structure.

anatomical

Create the folder (mkdir $basedir/input/anatomical) and paste the file inside.

t1w.nii.gz file coming from rtp-preproc output.

bval

Create the folder (mkdir $basedir/input/bval) and paste the file inside.

dwi.bval file coming from rtp-preproc output.

bvec

Create the folder (mkdir $basedir/input/bvec) and paste the file inside.

dwi.bvec file coming from rtp-preproc output.

dwi

Create the folder (mkdir $basedir/input/dwi) and paste the file inside.

dwi.nii.gz file coming from rtp-preproc output.

fs

Create the folder (mkdir $basedir/input/fs) and paste the file inside.

fs.zip file coming from freesurfer container output. See home page, it can be created/extended manually.

tractparams

Create the folder (mkdir $basedir/input/tractparams) and paste the file inside.

Create a comma separated values called tract_params.csv. Instruction and example, here.

Output files (todo, it can change)

There will be a big .zip file with all the outputs, and a bunch of other files:

• RTP_Output_afq_(datestam).zip: the whole output from the pipeline, zipped.
• afq_(datestamp).mat: the classical afq Matlab struct.
• .tck files: tracts to be visualized with mrTrix's mrView.
• .obj files: the same tracts, but in obj format. Can be visualized in the browser (for example, directly in Flywheel's output folder) or in macos's explorer.
• .mif file with the FoDs used in the whole brain tractogram tracking.
• .nii.gz files (some selected ones):
  • bo
  • fa
  • brainMask
  • wmMask
  • tensors