fc_compute_gbcd#

qx_mri.fc.fc_compute_gbcd(flist, command, roi, rcodes, nbands, mask, verbose, target, targetf, rsmooth, rdilate, ignore, time, method, weights, criterium)#

fc_compute_gbcd(flist, command, roi, rcodes, nbands, mask, verbose, target, targetf, rsmooth, rdilate, ignore, time, method, weights, criterium)

Computes GBC averages for each specified ROI for n bands defined as distance from ROI.

Parameters

--flist (str):

A conc-like style list of session image files or conc files:

  • session id:<session_id>

  • roi:<path to the individual's ROI file>

  • file:<path to bold files - one per line>

or a well strucutured string (see general_read_file_list).

--command (str):

The type of gbc to run: mFz, aFz, pFz, nFz, aD, pD, nD, mFzp, aFzp, ...

<type of gbc>:<parameter>|<type of gbc>:<parameter> ...

Following options are available:

  • 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.

--roi (str):

The roi names file.

--rcodes (vector, default ''):

Codes of regions from roi file to compute GBC for (all if not provided or left empty).

--nbands (int, default ''):

Number of distance bands to compute GBC for.

--mask (int | logical | vector, default ''):

An array mask defining which frames to use (1) and which not (0). All if empty.

--verbose (bool, default false):

Report what is going on.

--target (vector, default FreeSurfer scortex codes):

Array of ROI codes that define target ROI.

--targetf (str, default ''):

Target folder for results.

--rsmooth (int, default ''):

Radius for smoothing (no smoothing if empty).

--rdilate (int, default ''):

Radius for dilating mask (no dilation if empty).

--ignore (str, default 'usevec'):

The column in *_scrub.txt file that matches bold file to be used for ignore mask.

--time (bool, default true):

Whether to time the processing.

Notes

This is a wrapper function for computing GBC for specified ROI across the specified number of distance bands. The function goes through a list of sessions specified by flist file and runs img_compute_gbcd method on bold files listed for each session. ROI to compute GBC for are specified in roi and rcodes parameters, whereas the mask of what voxels to compute GBC over is specified by target parameter. The values should match rcodes used in session specific roi file. Usually this would be a freesurfer segmentation image and if no target values are specified all the gray matter related values present in aseg files are used.

The results are aggregated and stored in a matlab data file which holds a data structure with the following fields:

  • data.gbcd(s).gbc

    resulting GBC matrix for each session

  • data.gbcd(s).roiinfo

    names of ROI for which the GBC was computed for

  • data.gbcd(s).rdata

    information on center mass and distance bands for each of the ROI

  • data.roifile

    the file used to defined ROI

  • data.rcodes

    codes used to identify ROI

  • data.sessions

    cell array of session ids

targetf specifies the folder in which the results will be saved. The file will be named using the root of the flist with '_GBCd.mat' added to it.

For more specific information on what is computed, see help for nimage method img_compute_gbcd.

Examples

qunex fc_compute_gbcd \
    --flist='scz.list' \
    --command='mFz:0.1|pFz:0.1' \
    --roi='dlpfc.names' \
    --rcodes='[]' \
    --nbands=10 \
    --mask=0 \
    --verbose=true \
    --target='gray' \
    --targetf='dGBC' \
    --rsmooth=2 \
    --rdilate=2 \
    --ignore='udvarsme' \
    --time=false