Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add description of FoV and flip-angle choice #120

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

add description of FoV and flip-angle choice #120

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions source/MRI.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,19 +9,19 @@
<img src="./_static/mri/headcase.png" alt="head case" width="200" align="right" hspace="10"/> In order to minimize movement, each participant wears a custom-designed, personalized headcase during scanning, built by [Caseforge](https://caseforge.co). The headcases are milled based on a head scan of each participant generated using a handheld 3D scanner, and the shape of the MRI coil. Caseforge mills the personalized headcases in polystyrene foam blocks.

### Hearing protection
In order to provide an additional level of hearing protection against repeated exposure to the noise of the MR scanner, as well as optimize the quality of the auditory stimuli, we implemented two custom hearing protection set-ups for CNeuromod participants. The initial custom set-up was composed of the S15 MRI-compatible earphone system ([Sensimetric](http://www.sens.com/products/model-s15/)), standard-sized disposable Comply canal tips ([Hearing Components, Inc.](https://www.complyfoam.com/products/canal-tip); advertised Noise Reduction Rating: 29 dB), and modified commercial earmuffs ([Stanley Black & Decker Inc](https://www.stanleytools.com/product/rst-63007/leightning-l2f-premium-folding-earmuff); unmodified advertised Noise Reduction Rating: 27 dB). The commercial earmuffs were modified to render them thinner by cutting the inner section of the earmuff (i.e leaving the external cup intact) and re-attaching the foam ring (i.e. foam that seals around the ear) to the modified earmuff. This modification was necessary to enable the earmuffs to fit inside the head coil (i.e Siemen’s 64-channel), along with CaseForge headcases and the participants’ heads. This version of the custom hearing protection was eventually abandoned due to pressure points it caused on some participants' jaws, particularly individuals with larger heads, and when worn for extended periods of time (i.e 1h+).
In order to provide an additional level of hearing protection against repeated exposure to the noise of the MR scanner, as well as optimize the quality of the auditory stimuli, we implemented two custom hearing protection set-ups for CNeuromod participants. The initial custom set-up was composed of the S15 MRI-compatible earphone system ([Sensimetric](http://www.sens.com/products/model-s15/)), standard-sized disposable Comply canal tips ([Hearing Components, Inc.](https://www.complyfoam.com/products/canal-tip); advertised Noise Reduction Rating: 29 dB), and modified commercial earmuffs ([Stanley Black & Decker Inc](https://www.stanleytools.com/product/rst-63007/leightning-l2f-premium-folding-earmuff); unmodified advertised Noise Reduction Rating: 27 dB). The commercial earmuffs were modified to render them thinner by cutting the inner section of the earmuff (i.e leaving the external cup intact) and re-attaching the foam ring (i.e. foam that seals around the ear) to the modified earmuff. This modification was necessary to enable the earmuffs to fit inside the head coil (i.e Siemen’s 64-channel), along with CaseForge headcases and the participants’ heads. This version of the custom hearing protection was eventually abandoned due to pressure points it caused on some participants' jaws, particularly individuals with larger heads, and when worn for extended periods of time (i.e 1h+).

This initial hearing protection set-up was used by participants for the following datasets:(`hcptrt`),(`movie10`), (`friends`) seasons 1-4, and (`shinobi`).

The second, and current, custom hearing protection set-up is again composed of the S15 MRI-compatible earphone system (Sensimetrics Corporation), “custom” disposable Comply canal tips (Hearing Components, Inc., advertised Noise Reduction Rating: 29 dB), and headphone replacement memory foam rings (Brainwavz Audio). Additionally, each subject selected their “custom” Comply canal tip from one of two types of styles (original and short), each with three sizes (slim, standard, large), based on their ideal comfort level (i.e fit based on their ear canal shape) and relative sense of optimal sound protection.

The second version of the custom hearing protection set-up, which is still currently in use, was used by participants for the (`friends`) seasons 5-6 datasets.
The second version of the custom hearing protection set-up, which is still currently in use, was used by participants for the (`friends`) seasons 5-6 datasets.

## Sequences

### Functional sequences

The parameters of the functional MRI sequence relevant for data analysis can be found in the NeuroMod DataLad. The functional acquisition parameters are all identical to the one used in the `hcptrt` dataset. The Siemens exam card can be found [here](./_static/mri/functional_protocol_HCP-trt.pdf), and is briefly recapitulated below. Functional MRI data was acquired using an accelerated simultaneous multi-slice, gradient echo-planar imaging sequence [(Xu et al., 2013)](http://www.ncbi.nlm.nih.gov/pubmed/23899722) developed at the Center for Magnetic Resonance Research (CMRR) University of Minnesota, as part of the Human Connectome Project [(Glasser et al., 2016)](https://www.nature.com/articles/nn.4361). The sequence is available on the Siemens PRISMA scanner at UNF through a concept to production (C2P) agreement, and was used with the following parameters: slice acceleration factor = 4, TR = 1.49 s, TE = 37 ms, flip angle = 52 degrees, voxel size = 2 mm x 2 mm x 2 mm, 60 slices, acquisition matrix 96x96. In each session, a short acquisition (3 volumes) with reversed phase encoding direction was run to allow retrospective correction of B0 field inhomogeneity-induced distortion.
The parameters of the functional MRI sequence relevant for data analysis can be found in the NeuroMod DataLad. The functional acquisition parameters are all identical to the one used in the `hcptrt` dataset. The Siemens exam card can be found [here](./_static/mri/functional_protocol_HCP-trt.pdf), and is briefly recapitulated below. Functional MRI data was acquired using an accelerated simultaneous multi-slice, gradient echo-planar imaging sequence [(Xu et al., 2013)](http://www.ncbi.nlm.nih.gov/pubmed/23899722) developed at the Center for Magnetic Resonance Research (CMRR) University of Minnesota, as part of the Human Connectome Project [(Glasser et al., 2016)](https://www.nature.com/articles/nn.4361). The sequence is available on the Siemens PRISMA scanner at UNF through a concept to production (C2P) agreement, and was used with the following parameters: slice acceleration factor = 4, TR = 1.49 s, TE = 37 ms, flip angle = 52 degrees (based on Ernst angle calculation), voxel size = 2 mm x 2 mm x 2 mm, 60 slices, acquisition matrix 96x96. The field-of-view was set to cover the full brain (cerebrum and cerebellum) with an AC-PC -16° tilt. In each session, a short acquisition (3 volumes) with reversed phase encoding direction was run to allow retrospective correction of B0 field inhomogeneity-induced distortion.

### Brain anatomical sequences

Expand Down