How to deal with Ghosts in high-res EPI

Background

Ghost are the biggest limitation in high res fMRI. Similar to low resolution fMRI, ghosts in sub-millimeter EPI are arising from mismatch of k-space lines. This mismatch can be associated with (A) the actual readout itself or (B) inappropriate GRAPPA auto calibration data.

Here I try to make notes of strategies that I found helpful to minimize ghosts.

Continue reading “How to deal with Ghosts in high-res EPI”

Getting layers in EPI space

Overview

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 anatomical_maser.sh, see github)
  3. Running Freesurfer on MP2RAGE data in EPI space. (part of anatomical_maser.sh, see github)
  4. Using SUMA to get fine samples tissue borders in EPI-voxel space (in oblique space) (part of anatomical_maser.sh, 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

Intro

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 .

Sequence

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”

brain art

This is a collection of brain art that I made.

2018: You are your brain and your brain is us (Wax on plastic)

20180204_163914-01.jpeg 20180204_163903-01.jpeg

2018: Layer T-shirt

Screenshot 2018-01-27 11.05.46.png

2018: growing layers

GIF_2_TSHIRT.gif

2018: surfaces on volume

all_frames-01-01.png

2018 I am my brain and my brain is me

20180114_124338-01

2017 flow mapping in DC

flow_mapping.png

2017 Weapon of choice

20171125_095511-01

2016 Fingerprinting

20171125_160842-01.jpeg

2016 Fractal wax

20170226_114949-01

2017 Brain storming

20171125_095519-01

2017 Cajal

20171125_095508-01

2017 Weapon of choice and fractal brain tree

20171125_095456-01

2015: Bark

20171125_083302-01

2015: Brain roots

20171125_083240-01.jpeg

2016: Origami

20171125_082928-01

2015: Zwirbelnder Zwirn

20171125_082734-01

2016: Brain ball (Franklin Institute gift shop)

20171125_083115-01-01

2016: HAWAII

surf_gif

2016: Aborigines: They did equi-distant long before it was cool

aboriginal

2015: paper

20170528_221951-01.jpeg

2016: Future planning insecurity problems of foreign post doc in neuroscience: politics and money

20170806_213554-01-01.jpeg