parcellate_anat
parcellate_anat#
- qx_utilities.bash.parcellate_anat(sessionsfolder, session, inputdatatype, parcellationfile, outname, overwrite, extractdata)#
parcellate_anat
This function implements 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):
Delete prior run for a given session ('yes' / 'no').
- --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. 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 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>'