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', diffdata='/T1w/Diffusion/data.nii.gz')#

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, to use different data, you can use the diffdata parameter:

<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.

--diffdata (str, default '/T1w/Diffusion/data.nii.gz'):

Diffusion data 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#