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 signalprefix_referenceVolume.nii.gz
: reference volume with skullprefix_referenceVolumeBrain.nii.gz
: reference volume without skullprefix_segmenation.nii.gz
: segmentation tissuesprefix_struct.nii.gz
: T1w imageprefix_mask.nii.gz
: brain maskprefix_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 indexprefix_coregCrossCorr.txt
: Cross correlationprefix_coregDice.txt
: Dice indexprefix_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)