parcellate_anat

qx_utilities.bash.parcellate_anat(sessionsfolder, session, inputdatatype, parcellationfile, outname, extractdata, overwrite='no')

parcellate_anat

Run parcellation on the dense cortical thickness OR myelin files using a whole-brain parcellation (e.g. Glasser parcellation with subcortical labels included).

Parameters

--sessionsfolder (str):

Path to study data folder.

--session (str):

Comma separated list of sessions to run.

--inputdatatype (str):

Specify the type of dense data for the input file (e.g. MyelinMap_BC or corrThickness).

--parcellationfile (str):

Specify the absolute path of the ∗.dlabel file you want to use for parcellation.

--outname (str):

Specify the suffix output name of the pconn file.

--overwrite (str, default 'no'):

Whether to overwrite existing data (yes) or not (no). Note that previous data is deleted before the run, so in the case of a failed command run, previous results are lost.

--extractdata (flag):

Specify if you want to save out the matrix as a CSV file.

Examples

Run directly via:

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

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

Run via:

qunex parcellate_anat \\
    --<parameter1> \\
    --<parameter2> \\
    --<parameter3> ... \\
    --<parameterN>

NOTE: scheduler is available via qunex call:

--scheduler

A string for the cluster scheduler (e.g. 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 parcellate_anat \\
    --sessionsfolder='<folder_with_sessions>' \\
    --session='<case_id>' \\
    --inputdatatype='MyelinMap_BC' \\
    --parcellationfile='<dlabel_file_for_parcellation>' \\
    --overwrite='no' \\
    --extractdata='yes' \\
    --outname='<name_of_output_pconn_file>'