task module performs the General Linear Model (GLM) with FSL. It require a FSL-FEAT task design file with event files and full model setup. The task module run like FEAT-FMRI analysis and the ouputs is compatible with other xcpEngine modules such as roiquant, fcon and norm.

The six motion parameters are to be included in the FEAT design (by default) but can be changed as required by the user. The following motion nuissance regressors can be added : ‘36p’,’24p’,’acompcor’,’acompcor_gsr’,’aroma’, and ‘tcompcor’,see Ciric et al. 2017 for detail. This can be specify in the design file as:

task_vol2del[1]=0  # first N volume to be deleted
task_confound[1]='36p' # including 36 motion parameters

The Pipeline cohort file for the task can include a task design if the subjects’ event files are different:


if there are other nuissance regressors like physiological data that want to be included in the design, it can be added to the Pipeline cohort file as


Users can create a design file for each subject (or group) by running one subject in FSL GUI. This is a sample of a template design : https://github.com/PennBBL/xcpEngine/blob/master/utils/template.fsf for simple experiment of EYES OPEN versus EYES CLOSE

The outputs of task module is reorganized as follow::
  • task/fsl # the fsl feat directory
  • task/model # the supplied design files and model
  • task/logs # logs and html report
  • task/mc # motion parameters
  • task/copes # cope files depend on the design file and model setup
  • task/vacopes # varcope files depend on the design file and model setup
  • task/pes # arcope files depend on the design file and model setup
  • task/sigchange # % signal change computed from pes
  • task/stats # zstats files depend on the design file and model setup
The other outputs are derived directly from the FMRIPREP. The expected outputs include::
  • prefix_preprocessed.nii.gz: Bold signal
  • prefix_referenceVolume.nii.gz: reference volume with skull
  • prefix_referenceVolumeBrain.nii.gz: reference volume without skull
  • prefix_segmenation.nii.gz: segmentation tissues
  • prefix_struct.nii.gz: T1w image
  • prefix_mask.nii.gz: brain mask
  • prefix_fmriconf.tsv: confound regressors from ``FMRIPREP`
  • prefix_meanIntensity.nii.gz # average volume of the BOLD

All *nii.gz are expected to be have the same voxel size as the input but may have their orientation changed to the FSL standard.

The outputs also consist of Quality Assesmment between structrual and BOLD images::
  • prefix_coregCoverage.txt : Coverage index
  • prefix_coregCrossCorr.txt : Cross correlation
  • prefix_coregDice.txt : Dice index
  • prefix_coregJaccard.txt : Jaccard index

If the freesurfer is included as part of FMRIPREP outputs, the CIFTI files are produced for task and confound regressed bold data (res4d.nii.gz)