fc_compute_wrapper#

qx_utilities.bash.fc_compute_wrapper(calculation, runtype, targetf, flist, sessionsfolder, sessions, inputfiles, inputpath, outname, target, gbc, roinfo, extractdata, mask, overwrite='no', covariance='false', rsmooth='', rdilate='', verbose='false', time='false', vstep='1200', method='mean', options='all', ignore='', mem='4')#

fc_compute_wrapper

This function implements Global Brain Connectivity (GBC) or seed-based functional connectivity (FC) on the dense or parcellated (e.g. Glasser parcellation).

For more detailed documentation run <help fc_compute_gbc3>, <help nimage.img_compute_gbc> or <help fc_compute_seedmaps_multiple> inside MATLAB.

Parameters

--calculation (str):

Run <seed>, <gbc> or <dense> calculation for functional connectivity.

--runtype (str):

Run calculation on a <list> (requires a list input), on 'individual' sessions (requires manual specification) or a 'group' of individual sessions (equivalent to a list, but with manual specification).

--targetf (str):

Specify the absolute path for output folder. If using --runtype='individual' and left empty the output will default to --inputpath location for each session.

--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.

--covariance (str, default 'false'):

Whether to compute covariances instead of correlations ('true' / 'false').

--flist (str):

Specify ∗.list file of session information. If specified then --sessionsfolder, --inputfile, --session and --outname are omitted.

--sessionsfolder (str):

Path to study sessions folder.

--sessions (str):

Comma separated list of sessions to run.

--inputfiles (str):

Specify the comma separated file names you want to use (e.g. /bold1_Atlas_MSMAll.dtseries.nii,bold2_Atlas_MSMAll.dtseries.nii).

--inputpath (str):

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

--outname (str):

Specify the suffix name of the output file name.

--target (str, default detailed below):

Array of ROI codes that define target ROI. Defaults to FreeSurfer cortex codes.

--rsmooth (str, default ''):

Radius for smoothing (no smoothing if empty).

--rdilate (str, default ''):

Radius for dilating mask (no dilation if empty).

--gbc-command (str):

Specify the the type of gbc to run. This is a string describing GBC to compute. E.g. 'mFz:0.1|mFz:0.2|aFz:0.1|aFz:0.2|pFz:0.1|pFz:0.2'

mFz:t: computes mean Fz value across all voxels (over threshold t)
aFz:t: computes mean absolute Fz value across all voxels (over threshold t)
pFz:t: computes mean positive Fz value across all voxels (over threshold t)
nFz:t: computes mean positive Fz value across all voxels (below threshold t)
aD:t: computes proportion of voxels with absolute r over t
pD:t: computes proportion of voxels with positive r over t
nD:t: computes proportion of voxels with negative r below t
mFzp:n: computes mean Fz value across n proportional ranges
aFzp:n: computes mean absolute Fz value across n proportional ranges
mFzs:n: computes mean Fz value across n strength ranges
pFzs:n: computes mean Fz value across n strength ranges for positive correlations
nFzs:n: computes mean Fz value across n strength ranges for negative correlations
mDs:n: computes proportion of voxels within n strength ranges of r
aDs:n: computes proportion of våoxels within n strength ranges of absolute r
pDs:n: computes proportion of voxels within n strength ranges of positive r
nDs:n: computes proportion of voxels within n strength ranges of negative r.

--verbose (str, default 'false'):

Report what is going on.

--time (str, default 'false'):

Whether to print timing information.

--vstep (str, default '1200'):

How many voxels to process in a single step.

--roinfo (str):

An ROI file for the seed connectivity.

--method (str, default 'mean'):

Method for extracting timeseries - 'mean' or 'pca'.

--options (str, default 'all'):

A string defining which session files to save. Default assumes all:

'r' ... save map of correlations
'f' ... save map of Fisher z values
'cv' ... save map of covariances
'z' ... save map of Z scores.

--extractdata (str):

Specify if you want to save out the matrix as a CSV file (only available if the file is a ptseries).

--ignore (str, default ''):

The column in ∗_scrub.txt file that matches bold file to be used for ignore mask. All if empty.

--mask (str):

An array mask defining which frames to use (1) and which not (0). All if empty. If single value is specified then this number of frames is skipped.

--mem-limit (str, default '4'):

Restrict memory. Memory limit expressed in gigabytes.

Examples

Run directly via:

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

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

Run via:

qunex fc_compute_wrapper \
    --<parameter1> \
    --<parameter2> ... \
    --<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 fc_compute_wrapper \
    --sessionsfolder='<folder_with_sessions>' \
    --calculation='seed' \
    --runtype='individual' \
    --sessions='<comma_separarated_list_of_cases>' \
    --inputfiles='<files_to_compute_connectivity_on>' \
    --inputpath='/images/functional' \
    --extractdata='yes' \
    --ignore='udvarsme' \
    --roinfo='ROI_Names_File.names' \
    --options='' \
    --method='' \
    --targetf='<path_for_output_file>' \
    --mask='5' \
    --covariance='false'

qunex fc_compute_wrapper \
    --sessionsfolder='<folder_with_sessions>' \
    --runtype='list' \
    --flist='sessions.list' \
    --extractdata='yes' \
    --outname='<name_of_output_file>' \
    --ignore='udvarsme' \
    --roinfo='ROI_Names_File.names' \
    --options='' \
    --method='' \
    --targetf='<path_for_output_file>' \
    --mask='5' \
    --covariance='false'

qunex fc_compute_wrapper \
    --sessionsfolder='<folder_with_sessions>' \
    --calculation='gbc' \
    --runtype='individual' \
    --sessions='<comma_separarated_list_of_cases>' \
    --inputfiles='bold1_Atlas_MSMAll.dtseries.nii' \
    --inputpath='/images/functional' \
    --extractdata='yes' \
    --outname='<name_of_output_file>' \
    --ignore='udvarsme' \
    --gbc-command='mFz:' \
    --targetf='<path_for_output_file>' \
    --mask='5' \
    --target='' \
    --rsmooth='0' \
    --rdilate='0' \
    --verbose='true' \
    --time='true' \
    --vstep='10000' \
    --covariance='false'

qunex fc_compute_wrapper \
    --sessionsfolder='<folder_with_sessions>' \
    --calculation='gbc' \
    --runtype='list' \
    --flist='sessions.list' \
    --extractdata='yes' \
    --outname='<name_of_output_file>' \
    --ignore='udvarsme' \
    --gbc-command='mFz:' \
    --targetf='<path_for_output_file>' \
    --mask='5' \
    --target='' \
    --rsmooth='0' \
    --rdilate='0' \
    --verbose='true' \
    --time='true' \
    --vstep='10000' \
    --covariance='false'

QuNex documentation

fc_compute_wrapper

fc_compute_wrapper#