fc_compute_seedmaps_multiple#

qx_mri.fc.fc_compute_seedmaps_multiple(flist, roiinfo, inmask, options, targetf, method, ignore, cv)#

fc_compute_seedmaps_multiple(flist, roiinfo, inmask, options, targetf, method, ignore, cv)

Computes seed based correlations maps for individuals as well as group maps.

Parameters

--flist (str):

A .list file of session information, or a well strucutured string (see general_read_file_list).

--roinfo (str):

An ROI file.

--inmask (matrix | string, default ''):

Either an array mask defining which frames to use (1) and which not (0) or an event string specifying the events and frames to extract.

--options (str, default ''):

A string defining which session files to save:

  • r - save map of correlations

  • f - save map of Fisher z values

  • cv - save map of covariances

  • z - save map of Z scores

  • [] - no files are saved.

--targetf (str, default '.'):

The folder to save images in.

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

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

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

Do we omit frames to be ignored:

  • no - do not ignore any additional frames

  • event - ignore frames as marked in .fidl file

  • other - the column in ∗_scrub.txt file that matches bold file to be used for ignore mask.

--cv (bool, default false):

Whether covariances should be computed instead of correlations.

Output files

Function saves the following group files:

_group_Fz

average Fz over all the sessions

_group_r

average Fz converted back to Pearson r

_group_Z

p values converted to Z scores based on t-test testing if Fz over session differ significantly from 0 (two-tailed)

_all_Fz

Fz values of all the participants

_group_cov

average covariance

_all_cov

covariances of all the participants.

Notes

The function computes seedmaps for the specified ROI and saves group results as well as any specified individual results.

Examples

qunex fc_compute_seedmaps_multiple \
    --flist='con.list' \
    --roinfo='DMN.names' \
    --inmask=0 \
    --targetf=mean \
    --method=udvarsme \
    --ignore=false