dwi_pre_tractography

qx_utilities.bash.dwi_pre_tractography(sessionsfolder, sessions, diffusion_folder)

dwi_pre_tractography

Run the Pretractography Dense trajectory space generation.

Warning

This is a very quick function to run (less than 5min) so no overwrite options exist.

It explicitly assumes the Human Connectome Project folder structure for preprocessing and completed diffusion and bedpostX processing.

DWI data needs to be in the following folder:

<study_folder>/<session>/hcp/<session>/T1w/Diffusion

BedpostX output data needs to be in the following folder:

<study_folder>/<case>/hcp/<case>/T1w/Diffusion.bedpostX

This can be changed via the --diffusion_folder parameter.

Parameters

--sessionsfolder (str):

Path to study folder that contains sessions.

--sessions (str):

Comma separated list of sessions to run.

--diffusion_folder (str):

Path to the diffusion folder.

Examples

qunex dwi_pre_tractography \\
    --sessionsfolder='<path_to_study_sessions_folder>' \\
    --sessions='<comma_separarated_list_of_cases>' \\
    --scheduler='<name_of_scheduler_and_options>'

Direct usage:

$0 <StudyFolder> <Session> <MSMflag>

T1w and MNINonLinear folders are expected within <StudyFolder>/<Session>.

MSMflag=0 uses the default surfaces, MSMflag=1 uses the MSM surfaces defined in make_trajectory_space_mni.sh.