Motivation:

To detail the fMRI processing of CONTE using the XCP Engine on CFN. Both structural (ANTS, jlf, gmd) and functional (fear conditioning run1) data were processed using the XCP Engine. This wiki does not detail how the XCP Engine works, it merely serves as a log to point to output, cohort files, and design files. For more information on the pipeline please see the XCP Engine Wiki.

Structural XCP Engine:

The structural pipeline was run to obtain cortical thickness (ANTS), gray matter density (gmd), and volume (jlf) from CONTE structural data.

The cohort file (subject list) given to the engine contains all version3 subjects with structural data (n118). It simply lists the bblid, datexscanid, and path to the MPRAGE nifti for each subject. It lives here:

    /data/joy/BBL/projects/conteReproc2017/xcpStructural/cohort_file_design3_n118.csv    

The templates used were the PNC templates here:

   /data/joy/BBL/studies/pnc/template/pnc_template_brain.nii.gz    

The output for is bblid/datexscanid specific directories in the following directory:

   /data/joy/BBL/studies/conte/processedData/structural/conte_design3_n118_structural_201706051547       

The design file used is here:

    /data/joy/BBL/applications/xcpEngine/designs/conte_design3_n118_structural_201706051547.dsn   

And run using the following command:

     /home/mquarmley/xcpEngine/xcpEngine -d /data/joy/BBL/applications/xcpEngine/designs/conte_design3_n118_structural_201706051547.dsn -m c -t    

All further information about the parameters used to run the Structural XCP Engine for CONTE is in the design file above. Again, please see the XCP Engine wiki for more information on interpreting the design file.

Functional XCP Engine: