dwi_seed_tractography_dense

qx_utilities.bash.dwi_seed_tractography_dense(sessionsfolder, sessions, matrixversion, seedfile, outname, overwrite, waytotal='none')

dwi_seed_tractography_dense

This function implements reduction on the DWI dense connectomes using a given 'seed' structure (e.g. thalamus).

It explicitly assumes the the Human Connectome Project folder structure for preprocessing. Dense Connectome DWI data needs to be in the following folder:

<folder_with_sessions>/<case>/hcp/<case>/MNINonLinear/Results/Tractography/

It produces the following outputs:

• Dense connectivity seed tractography file: <folder_with_sessions>/<case>/hcp/<case>/MNINonLinear/Results/Tractography/<session>_Conn<matrixversion>_<outname>.dconn.nii

• Dense scalar seed tractography file: <folder_with_sessions>/<case>/hcp/<case>/MNINonLinear/Results/Tractography/<session>_Conn<matrixversion>_<outname>_Avg.dscalar.nii

Parameters

--sessionsfolder (str):

Path to study folder that contains sessions.

--sessions (str):

Comma separated list of sessions to run.

--matrixversion (str):

Matrix solution version to run parcellation on; e.g. 1 or 3.

--seedfile (str):

Specify the absolute path of the seed file you want to use as a seed for dconn reduction (e.g. <study_folder>/<case>/hcp/<case>/MNINonLinear/Results/Tractography/CIFTI_STRUCTURE_THALAMUS_RIGHT.nii.gz). Note: If you specify --seedfile='gbc' then the function computes an average across all streamlines from every greyordinate to all other greyordinates.

--outname (str):

Specify the suffix output name of the dscalar file.

--overwrite (str):

Delete prior run for a given session ('yes' / 'no').

--waytotal (str, default 'none'):

Use the waytotal normalized version of the DWI dense connectome. Default:

• 'none' ... without waytotal normalization

• 'standard' ... standard waytotal normalized

• 'log' ... log-transformed waytotal normalized.

Examples

Run directly via:

${TOOLS}/${QUNEXREPO}/bash/qx_utilities/dwi_seed_tractography_dense.sh \
    --<parameter1> \
    --<parameter2> \
    --<parameter3> ... \
    --<parameterN>

NOTE: --scheduler is not available via direct script call.

Run via:

qunex dwi_seed_tractography_dense \
    --<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_seed_tractography_dense \
    --sessionsfolder='<folder_with_sessions>' \
    --session='<case_id>' \
    --matrixversion='3' \
    --seedfile='<folder_with_sessions>/<case>/hcp/<case>/MNINonLinear/Results/Tractography/CIFTI_STRUCTURE_THALAMUS_RIGHT.nii.gz' \
    --overwrite='no' \
    --outname='THALAMUS'