fc_compute_gbc3#

qx_mri.fc.fc_compute_gbc3(flist, command, mask, verbose, target, targetf, rsmooth, rdilate, ignore, time, cv, vstep)#

fc_compute_gbc3(flist, command, mask, verbose, target, targetf, rsmooth, rdilate, ignore, time, cv, vstep)

Computes GBC maps for individuals as well as group maps.

Parameters

--flist (str):

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

  • 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

  • aFzs:n

    computes mean absolute Fz value across n strength ranges

  • mDs:n

    computes proportion of voxels within n strength ranges of r

  • aDs:n

    computes proportion of voxels 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.

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

A 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 cortex codes):

Array of ROI codes that define target ROI.

--targetf (str):

Path to 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 ''):

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

--time (bool, default false):

Whether to print timing information.

--cv (bool, default false):

Whether to compute covariances instead of correlations.

--vstep (int, default 1200):

How many voxels to process in a single step.

Notes

This function is a wrapper for nimage.img_compute_gbc method. It enables computing GBC for a list of sessions. flist specifies the session identities, bold files to compute GBC on and roi to use for specifying the volume mask, voxels over which to compute GBC. mask specifies what frames of an image to work on. target specifies the ROI codes that define ROI from the session specific ROI files over which to compute GBC for. Usually the session specific roi file would be that session's FreeSurfer aseg or aseg+aparc segmentation. And if no target is specified all gray matter voxels are used for computing GBC.

What specifically gets computed is defined in the command string. For specifics see help for the nimage.img_compute_gbc method.

In addition, if rsmoot and rdilate are specified, each sessions bold image will be 3D smoothed with the specifed FWHM in voxels. As sessions gray matter masks differ and do not overlap precisely, rdilate will dilate the borders with the provided number of voxels. Here it is important to note that values from the expanded mask will not be used, rather the values from the valid mask will be smeared into the dilated area.

The results will be saved in the targetf folder. The results of each command will be saved in a separate file holding the computed GBC values for all the sessions. The files will be named with the root of the flist with _gbc_ and code for the specific gbc computed added.

For more information see documentation for nimage.img_compute_gbc method.

Examples

qunex fc_compute_gbc3 \
    --flist='scz.list' \
    --command='mFz:0.1|pFz:0.1|mFz:0.1|pD:0.3|mD:0.3' \
    --mask=0 \
    --verbose=true \
    --target=gray \
    --targetf=GBC \
    --rsmooth=2 \
    --rdilate=2 \
    --ignore=udvarsme \
    --time=true \
    --cv=true