Merge branch 'master' of https://github.com/courtois-neuromod/cneurom…

…od_docs

source/MRI.md

@@ -1,13 +1,29 @@
 # MRI
 
-Magnetic resonance imaging (MRI) for the Courtois neuromod project is being acquired at the functional neuroimaging unit ([UNF](https://unf-montreal.ca/)), located at the "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal" ([CRIUGM](http://www.criugm.qc.ca/)) and affiliated with [Université de Montréal](https://www.umontreal.ca/) as well as the [CIUSSS du Centre-Sud-de-l'île-de-Montréal](https://ciusss-centresudmtl.gouv.qc.ca/propos/services-en-anglais). The scanner is a Siemens Prisma fit, with a 64 channels head coil. Most imaging in the Courtois Neuromod project are composed solely of functional MRI runs. Periodically, an entire session is dedicated to anatomical scans. The scanning environment includes a number of stimulation and response equipment, detailed below.   
+Magnetic resonance imaging (MRI) for the Courtois neuromod project is being acquired at the functional neuroimaging unit ([UNF](https://unf-montreal.ca/)), located at the "Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal" ([CRIUGM](http://www.criugm.qc.ca/)) and affiliated with [Université de Montréal](https://www.umontreal.ca/) as well as the [CIUSSS du Centre-Sud-de-l'île-de-Montréal](https://ciusss-centresudmtl.gouv.qc.ca/propos/services-en-anglais). The scanner is a Siemens Prisma Fit, with a 64 channels head coil. Most imaging in the Courtois Neuromod project are composed solely of functional MRI runs. Periodically, an entire session is dedicated to anatomical scans. The scanning environment includes a number of stimulation and response equipment, detailed below.   
 
 ## Personalized head cases
 <img src="./_static/mri/headcase.png" alt="head case" width="200" align="right" hspace="10"/> In order to minimize movement during neuroimaging scans, each participant wears a custom-designed, personalized headcase built by a company called [Caseforge](https://caseforge.co) during scanning. The headcase are milled based on a scan of each participant's head generated using a handheld 3D scanner, as well as the shape of the MRI coil. Caseforge  mills the personalized headcases in foam blocks.
 
-## Auditory stimuli
+## Stimuli
 
-## Visual stimuli
+### Visual presentation
+
+All visual stimuli were presented with a projector onto a blank screen located in the MRI room, through a waveguide.
+
+### Auditory system
+
+For functional sessions, participant are equipped with MRI compatible headphone inserts.
+On the computer used for stimuli presentation, a custom impulse response of the headphones is applied with an online finite impulse response filter using the LADSPA DSP to all the presented stimuli.
+This impulse response was provided by the manufacturer.
+
+### HCPTRT Stimuli
+
+Eprime scripts provided by the Human Connectome project were adapted for our presentation system and used in the study
+
+### Other stimuli
+
+A custom overlay on top of Psychopy was used to present the different tasks and synchronize task with the scanner TTL.
 
 ## Video  game controller
 
@@ -25,6 +41,7 @@ The Siemens pdf exam card of the anatomical sessions can be found [here](./_stat
 
 ### Brain
 
+
 Localizer:          ~0:21
 ANA T1W:             6:38
 ANA T2W:             5:57
@@ -38,6 +55,9 @@ T2_SWI_TRA_P2_!5MM:  4:54
 
 
 ### Cervical spinal cord
+
+A detailed description of the protocol can be found here: [Spinal Cord MRI Protocols](https://osf.io/tt4z9/), including sequences ported to other MRI manufacturers.
+
 Localizer:         ~0:21
 T2W:                4:02
 *DWI gated:        ~2:12