Getting layers in EPI space


Big steps:

  1. Manual aligment of MP2RAGE with EPI (optional when MP2RAGE is acquired in same session)
  2. ANTS alignment of MP2RAGE and EPI. (part of, see github)
  3. Running Freesurfer on MP2RAGE data in EPI space. (part of, see github)
  4. Using SUMA to get fine samples tissue borders in EPI-voxel space (in oblique space) (part of, see github)
  5. Manual correction of Freesurfer GM-ribbon
  6. calculating layers from GM-ribbon in neuroDebian.

Continue reading “Getting layers in EPI space”

Motion and BOLD correction in SS-SI-VASO


This is a description on how to use SPM and/or AFNI for high-resolution SS-SI-VASO data evaluations.

Here it is explained what to do with the raw fMTR data from the scanner to obtain CBV and BOLD signal time courses .


Every other image has a different contrast.

Screenshot 2017-11-25 15.27.14.png

Continue reading “Motion and BOLD correction in SS-SI-VASO”