dwi_dtifit
dwi_dtifit#
- qx_utilities.bash.dwi_dtifit(sessionsfolder, session, overwrite, species, cni, sse, wls, kurt, kurtdir, littlebit, save_tensor, zmin, zmax, ymin, ymax, xmin, xmax, gradnonlin, scheduler, mask='T1w/Diffusion/nodif_brain_mask', bvecs='T1w/Diffusion/bvecs', bvals='T1w/Diffusion/bvals')#
dwi_dtifit
This function runs the FSL dtifit processing locally or via a scheduler. It explicitly assumes the Human Connectome Project folder structure for preprocessing and completed diffusion processing.
The DWI data is expected to be in the following folder:
<study_folder>/<session>/hcp/<session>/T1w/Diffusion
Parameters
- --sessionsfolder (str):
Path to study folder that contains sessions.
- --session (str):
The sessions to run.
- --overwrite (str):
Delete prior run for a given session ('yes' / 'no').
- --species (str):
dtifit currently supports processing of human and macaqu data. If processing macaques set this parameter to macaque.
- --mask (str, default 'T1w/Diffusion/nodif_brain_mask'):
Set binary mask file.
- --bvecs (str, default 'T1w/Diffusion/bvecs'):
b vectors file.
- --bvals (str, default 'T1w/Diffusion/bvals'):
b values file.
- --cni (str):
Input confound regressors [not set by default].
- --sse (str):
Output sum of squared errors [not set by default].
- --wls (str):
Fit the tensor with weighted least square [not set by default].
- --kurt (str):
Output mean kurtosis map (for multi-shell data [not set by default].
- --kurtdir (str):
Output parallel/perpendicular kurtosis map (for multi-shell data) [not set by default].
- --littlebit (str):
Only process small area of brain [not set by default].
- --save_tensor (str):
Save the elements of the tensor [not set by default].
- --zmin (str):
Min z [not set by default].
- --zmax (str):
Max z [not set by default].
- --ymin (str):
Min y [not set by default].
- --ymax (str):
Max y [not set by default].
- --xmin (str):
Min x [not set by default].
- --xmax (str):
Max x [not set by default].
- --gradnonlin (str):
Gradient nonlinearity tensor file [not set by default].
- --scheduler (str):
A string for the cluster scheduler (e.g. LSF, PBS or SLURM) followed by relevant options; e.g. for SLURM the string would look like this:
--scheduler='SLURM,jobname=<name_of_job>,time=<job_duration>,cpus-per-task=<cpu_number>,mem-per-cpu=<memory>,partition=<queue_to_send_job_to>'
Examples
Run directly via:
${TOOLS}/${QUNEXREPO}/bash/qx_utilities/dwi_dtifit.sh \ --<parameter1> \ --<parameter2> \ --<parameter3> ... \ --<parameterN>
NOTE: --scheduler is not available via direct script call.
Run via:
qunex dwi_dtifit \ --<parameter1> \ --<parameter2> ... \ --<parameterN>
NOTE: scheduler is available via qunex call.
- --scheduler
A string for the cluster scheduler (e.g. LSF, PBS or SLURM) followed by relevant options.
For SLURM scheduler the string would look like this via the qunex call:
--scheduler='SLURM,jobname=<name_of_job>,time=<job_duration>,cpus-per-task=<cpu_number>,mem-per-cpu=<memory>,partition=<queue_to_send_job_to>'
qunex dwi_dtifit \ --sessionsfolder='<path_to_study_sessionsfolder>' \ --session='<session_id>' \ --scheduler='<name_of_scheduler_and_options>' \ --overwrite='yes'