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”
The paper that explains the sequence and its parameter regime is can be found here: https://www.ncbi.nlm.nih.gov/pubmed/23963641. The sequence diagram looks something like this:
Continue reading “SS-SI-VASO Sequence Manual”
- Manual aligment of MP2RAGE with EPI (optional when MP2RAGE is acquired in same session)
- ANTS alignment of MP2RAGE and EPI. (part of anatomical_maser.sh, see github)
- Running Freesurfer on MP2RAGE data in EPI space. (part of anatomical_maser.sh, see github)
- Using SUMA to get fine samples tissue borders in EPI-voxel space (in oblique space) (part of anatomical_maser.sh, see github)
- Manual correction of Freesurfer GM-ribbon
- calculating layers from GM-ribbon in neuroDebian.
Continue reading “Getting layers in EPI space”
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.
Continue reading “Motion and BOLD correction in SS-SI-VASO”
This is a collection of brain art that I made.
2018: You are your brain and your brain is us (Wax on plastic)
2018: Layer T-shirt
2018: growing layers
2018: surfaces on volume
2018 I am my brain and my brain is me
2017 flow mapping in DC
2017 Weapon of choice
2016 Fractal wax
2017 Brain storming
2017 Weapon of choice and fractal brain tree
2015: Brain roots
2015: Zwirbelnder Zwirn
2016: Brain ball (Franklin Institute gift shop)
2016: Aborigines: They did equi-distant long before it was cool
2016: Future planning insecurity problems of foreign post doc in neuroscience: politics and money