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'

QuNex documentation

dwi_dtifit

dwi_dtifit#