Boutiques Descriptors

[gkiar]

For this project we need the following Boutiques descriptors generated:

• [ ] FSL's feat

  This tool is called with feat <my_configuration_file.fsf>. A template .fsf file can be generated using the GUI for feat, or obtained from the HCP preprocessed task-fMRI derivatives folders. The command-line should be specified as above, and an output-file should be the configuration file which is populated by input values, of course specified as inputs. For default values of feat, is it more reliable to generate this template using the GUI rather than adopt those used in HCP as the defaults. An example can also be found here.

• [ ] AFNI's afni_proc.py

  This tool is called with afni_proc.py and various command-line arguments. This list is very long, so for starters we should just describe those that are necessary for our experiments. We can start from an example found here for our first pass, and then see if there are any holes for the other analyses in this repository, and finally touch base with the AFNI devs about other options that are good to add before publishing our "final" version.

• [ ] SPM: TBD

I will add a similar issue for diffusion tools, soon. @DarrinFong, if you're up for it, it would be great to have your help making these descriptors! I think it'd be a good way to help you get familiar with how we handle configuration files, and wrap two incredibly useful tools for fMRI analysis to our published collection. Are you interested?

cc: @glatard @cmaumet

[gkiar]

• [ ] Every tool used in this tutorial: http://userdocs.mrtrix.org/en/latest/getting_started/beginner_dwi_tutorial.html

[glatard]

For mrtrix3:

• Ignore mrview
• Possible starting points for containerization: https://github.com/MRtrix3/mrtrix3/pull/446 or https://github.com/MRtrix3/mrtrix3/pull/1372
• See also glatard/mrtrix3 or brainlife/mrtrix3 or kaczmarj/mrtrix3 on Dockerhub

[gkiar]

• [ ] For FSL diffusion: those listed here, in particular: bedpostx, probtrackx, dtifit

Use the following container for the above: https://hub.docker.com/r/gkiar/fsl_5.0.11_dwi_preprocessing

[gkiar]

When they're ready, @DarrinFong, please PR them into the following directories: https://github.com/gkiar/stability/tree/master/code/tractography