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Rest CBF Coupling

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Lauren Beard edited this page Jun 20, 2018 · 9 revisions

Alff-Cbf and Reho-Cbf Coupling

Note: both volumetric and surface coupling are discussed in this wiki. Volumetric coupling is carried out using Kristin Linn's imco package and results in nii.gz output.

Surface

Surface projections

Surface projections are carried out using freesrufer version 6. Please refer to this wiki for more information on surface projections: https://github.com/PennBBL/tutorials/wiki/3D-Volume-to-Surface-Projection-(FS)

Code: /data/jux/BBL/projects/coupling/imcoScripts/surfProjection/*

Output

  • Alff: /data/jux/BBL/projects/coupling/surfaceMaps/alff
  • Reho: /data/jux/BBL/projects/coupling/surfaceMaps/reho
  • Cbf: /data/jux/BBL/projects/coupling/surfaceMaps/cbf

Surface coupling

Surface level coupling is carried out using freesurfer and results in surface (.mgh) and text (.asc) output. These are organized by hemisphere within each coupling directory. Please refer to this wiki for more information on surface coupling: https://github.com/PennBBL/tutorials/wiki/Surface-Coupling

Code: /data/jux/BBL/projects/coupling/imcoScripts/surfCoupling/R

Output

  • Alff-Cbf directory: /data/jux/BBL/projects/coupling/couplingSurfaceMaps/alffCbf/
  • Reho-Cbf: /data/jux/BBL/projects/coupling/couplingSurfaceMaps/rehoCbf/

Volumetric

Processing

Code: running volumetric coupling requires imco dependencies, cohort R scripts, and wrappers. The wrappers are used to submit the cohort files to the grid.

  • dependencies: /data/jux/BBL/projects/coupling/imcoScripts/restCbf/dependencies
  • cohorts: /data/jux/BBL/projects/coupling/imcoScripts/restCbf/cohorts
  • wrappers: /data/jux/BBL/projects/coupling/imcoScripts/restCbf/wrappers/

Submit wrapper: qsub -q qlogin.himem.q -N c10s3i -V /data/jux/BBL/projects/coupling/imcoScripts/restCbf/wrappers//wrapper_alff-cbf_size3_cohort10.sh

Example imco call:

fls = list()
fls[[1]] = alffNorm
fls[[2]] = cbfNorm

    imco(files=fls, brainMask=maskImg, subMask=NULL, type="regression", ref=1, fwhm=3, thresh=0.005, radius=3, reverse=FALSE, verbose=TRUE, retimg=FALSE, outDir=outdir)

Example imco call notes:

  • maskImg should also be a nifti or path
  • you probably won’t need the subMask argument unless you want to do testing on a subset of voxels in the brain mask
  • ref=1 means use the fls1 (alff in this case) as the dependent variable in the coupling regressions
  • I usually specify the neighborhood using the radius argument which overrides fwhm and thresh
  • reverse=TRUE will give you regressions of both ALFF on CBF and CBF on ALFF
  • outDir specifies where to write the output images

Output

ALFF-CBF maps:

  • Size 3: /data/jux/BBL/projects/coupling/couplingMaps/alff_cbf_size3_20180209/
  • Size 4: /data/jux/BBL/projects/coupling/couplingMaps/alff_cbf_size4_20180209/

GMD-CBF maps (run by Kristin Linn):

  • Size 3: /data/jux/BBL/projects/coupling/couplingMaps/gmd_cbf/gmd_cbf_size3
  • Size 4: /data/jux/BBL/projects/coupling/couplingMaps/gmd_cbf/gmd_cbf_size4

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