`task`¶

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

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

id0,img,task_design
sub-01,/path/to/bold1.nii.gz,/path/to/design1.fsf
sub-02,/path/to/bold2.nii.gz,/path/to/design2.fsf
sub-04,/path/to/bold4.nii.gz,/path/to/design4.fsf

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

id0,img,task_design,task_custom
sub-01,/path/to/bold1.nii.gz,/path/to/design1.fsf,/path/to/custom.txt

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)

task¶

`task`¶