parcellate_bold

qx_utilities.bash.parcellate_bold(sessionsfolder, sessions, inputfile, inputpath, inputdatatype, parcellationfile, singleinputfile, overwrite, outname, outpath, weightsfile, extractdata, computepconn='no', useweights='no')

parcellate_bold

This function implements parcellation on the BOLD dense files using a whole-brain parcellation (e.g. Glasser parcellation with subcortical labels included).

Parameters

--sessionsfolder (str):

Path to study folder that contains sessions.

--sessions (str):

Comma separated list of sessions to run.

--inputfile (str):

Specify the name of the file you want to use for parcellation (e.g. 'bold1_Atlas_MSMAll_hp2000_clean').

--inputpath (str):

Specify path of the file you want to use for parcellation relative to the master study folder and session directory (e.g. '/images/functional/').

--inputdatatype (str):

Specify the type of data for the input file (e.g. 'dscalar' or 'dtseries').

--parcellationfile (str):

Specify the absolute path of the file you want to use for parcellation (e.g. '/gpfs/project/fas/n3/Studies/Connectome/Parcellations/glasser_parcellation/LR_Colelab_partitions_v1d_islands_withsubcortex.dlabel.nii').

--singleinputfile (str):

Parcellate only a single file in any location. Individual flags are not needed (--session, --sessionsfolder, --inputfile).

--overwrite (str):

Delete prior run ('yes' / 'no').

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

Specify if a parcellated connectivity file should be computed (pconn). This is done using covariance and correlation ('yes' / 'no').

--outname (str):

Specify the suffix output name of the pconn file.

--outpath (str):

Specify the output path name of the pconn file relative to the master study folder (e.g. '/images/functional/').

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

If computing a parcellated connectivity file you can specify which frames to omit (e.g. 'yes' or 'no').

--weightsfile (str):

Specify the location of the weights file relative to the master study folder (e.g. '/images/functional/movement/bold1.use').

--extractdata (str):

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

Examples

Run directly via:

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

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

Run via:

qunex parcellate_bold \
    --<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 parcellate_bold \
    --sessionsfolder='<folder_with_sessions>' \
    --session='<session_id>' \
    --inputfile='<name_of_input_file' \
    --inputpath='<path_for_input_file>' \
    --inputdatatype='<type_of_dense_data_for_input_file>' \
    --parcellationfile='<dlabel_file_for_parcellation>' \
    --overwrite='no' \
    --extractdata='yes' \
    --outname='<name_of_output_pconn_file>' \
    --outpath='<path_for_output_file>'