NeuroPoly student feedback: Thomas Dagonneau

[tomDag25]

This issue is the global feedback for the mooc from Thomas Dagonneau. Disclaimer : I'm not a very good english speaker so I might see some typo where there are not or miss some.

[tomDag25]

Feedback for the ReadMe page :

• in 1.1 : maybe add (mOOC) after mini Open Online Course
• feels confusing to speak from a book in 1.2 section when you didn't mention anything about a book previously
• typo in 1.2 : Quantitative MRI (qMRI) aims to promises precise and reproducible measurements of tissue properties using MRI.
• typo in 1.3 : Leveraging the NeuroLibre platform, readers can access fully reproduce the material in this book and allows them to engage with real qMRI data through their web browser.
• typo in 1.3 space after the point : their web browser.This

Global feedback : Good first page : defines what is a mooc and the goal of the mooc

[tomDag25]

Feedback for Introduction to qMRI -> Basics of MRI and qMRI :

• in the See also : maybe put the name of the article instead of the year ? At first I didn't get that it was a link to the article and I thought the only link was to Nishimura wikipedia page

Global feedback : Clear

[mathieuboudreau]

Tagging @agahkarakuzu as chapter 1 was from his thesis I believe

[tomDag25]

Feedback for Introduction to qMRI -> The million dollar question:

• not sure if that's the goal but in 1.1 the MR acronym has not the same feature as MRI to explain its signification
• typo 1.1 : sug- gests (maybe it's normal I don't know much about written reports)
• Fig1 : would be clearer and easier to read if the conventional MRI was on the right side of the figure since you speak about it before. Else you have to read the figure in the opposite direction to the one suggested by the text. (Else the figure's content is good)
• typo in 1.1 : an- other

Global feedback : Loved the bean russian roulette example. The historical aspect is very interesting !

[tomDag25]

Feedback for Introduction to qMRI -> A pictorial and historic journey into how MRI works

• the figure numbers don't seem to be making reference to any figure in the section
• typo in 1.1.1 : However, in reality, we don’t have access to observe NMR effects at such a fine-grained level
• 1.1.1 : quantum-jitters -> I don't know what it is so maybe defining it or putting a link to the wikipedia would be great (don't know if it was planned since there is no link in this page)
• 1.1.1 : Schrödinger’s cat -> put the wikipedia link ? Don't know how obvious this illustration is
• FIg5 : maybe put it after the text citing it. When you read the page you don't really understand where it's coming from before the text about Bloch

Global feedback : Good ! In the version I reviewed most links where missing and also references but I think it's normal

[tomDag25]

Feedback for Introduction to qMRI -> Measuring and encoding the MRI signal

• there is no under-title like in other sections
• in 1.1 I feel like the reader could benefit from seeing the new equation after removing the components = 0 : In this case, the last two terms of the equation vanish, leaving the precessional component of the equation.
• numbers of cited equations don't refer to the numbers of the equations
• 1.2 : The analogy with the defibrillator is not presented the same way as the analogy with beans and dating (in a square highlighted)
• Fig4 : I know what you are talking about so I get it but maybe to emphasise what a gradient is you could put a graph under the MRI scanner showing how the value evolves according to z for example ?
• typo in 1.4 : ob- servations

Global feedback : Good ! In the version I reviewed most links where missing and also references but I think it's normal

[tomDag25]

Feedback for Introduction to qMRI -> Two MRI sequences and two qMRI measurements

• I feel like a bit of explanation for the difference between T2 and T2* could be appreciated. For now there is only : T2∗ – the effective T2
• typo at the end : con- ventional

Global feedback : Good, and I validate both musical bands !

[tomDag25]

Feedback for Introduction to qMRI -> Will qMRI take over the world?

• the figure numbers don't seem to be making reference to any figure in the section
• Fig1 : very nice Fig but I don't find it easy to understand
• typo in 1.1 : Figure 2.23 shows that all

qMRI methods share a common methodolog

• typo in 1.1 : chal- lenging
• 1.2 is just a title ?

Global feedback : Good, 1.2 is missing there is only the title.

[tomDag25]

Feedback for T1 Mapping -> Inversion recovery -> Introduction

• typo space after the point : inversion recoverytechnique
• the cited figures don't refer to existing figures
• change in the way to count figure between the Introduction to qMRI chapter and this one (figure 1 vs figure 2.1)

Global feedback : Good

[tomDag25]

Feedback for T1 Mapping -> Inversion recovery -> Signal Modelling

• typo : 5_T_1 (2 times)
• Fig2.3 : maybe choose a default value of T1 so that when you load the page there is a difference between the two curves ?

Global feedback : Good

[tomDag25]

Feedback for T1 Mapping -> Inversion recovery -> Data Fitting

• typo : 5_T_1, 1.5_T_1
• only paper without a link : Barral et al. 2010

Global feedback : Good

[tomDag25]

Feedback for T1 Mapping -> Inversion recovery -> Benefits and Pitfalls

• References formating changed : green arrow

Global feedback : Good

[tomDag25]

Feedback for T1 Mapping -> Inversion recovery -> Other Saturation-Recovery T1 Mapping techniques

Global feedback : Good

[tomDag25]

Feedback for T1 Mapping -> Variable Flip Angle -> Introduction

Global feedback : Good

[tomDag25]

Feedback for T1 Mapping -> Variable Flip Angle -> Signal Modelling

• typo : using Bloch simulations (orange) -> it's red
• I think the text after Figure 2.9 should be in the legend of the figure ?
• References with a green arrow

Global feedback : Good but not sure about the Fig 2.9 legend

[agahkarakuzu]

@tomDag25 thanks for the feedback! I will reflect these when it nears minor tweaks phase.

[tomDag25]

Feedback for T1 Mapping -> Variable Flip Angle -> Data fitting

• the link for linear least square doesn't work
• no figure 2.12 ?
• References with a green arrow
• Problem with the order of elements at the end of the page

Global feedback : Good but no figure 2.12

[tomDag25]

Feedback for T1 Mapping -> Variable Flip Angle -> Benefits and Pitfalls

Global feedback : Good

[tomDag25]

Feedback for T1 Mapping -> MP2RAGE -> Introduction

• Figure 1 -> No link and also no figure 1 ? Probably figure 2.14

Global feedback : good

[tomDag25]

Feedback for T1 Mapping -> MP2RAGE -> Signal Modelling

• in the following part I would keep using markdown for formatting, as a reader it feels strange to change in the middle of the text : no partial Fourier or parallel imaging acceleration), then these values are TA = TI1 - (n/2)TR, TB = TI2 - (TI1 + nTR), and TC = TRMP2RAGE - (TI1 + (n/2)TR), where n is the number of voxels acquired in the 3D phase encode direction varied within each GRE block. The value m{sub}`1z,ss is the steady-state longitudinal magnetization prior to the inversion pulse, and is given by:
• typo : From Equations 2.13, 2.14, 2.15, and 2.13

Global feedback : good but there seem to be a problem with the markdown in this page

[tomDag25]

Feedback for T1 Mapping -> MP2RAGE -> Data Fitting

• no link : (e.g. Levenberg-Marquardt)
• the whole paragraph is allready in the Introduction : MP2RAGE is an extension of the conventional MPRAGE pulse sequence widely used in clinical studies Haase et al., 1989Mugler & Brookeman, 1990. A simplified version of the MP2RAGE pulse sequence is shown in Figure 2.14. MP2RAGE can be seen as a hybrid between the inversion recovery and VFA pulse sequences: a 180° inversion pulse is used to prepare the magnetization for T1 sensitivity at the beginning of each TRMP2RAGE, and then two images are acquired at different inversion times using gradient recalled echo (GRE) imaging blocks with low flip angles and short repetition times (TR). During a given GRE imaging block, each excitation pulse is followed by a constant in-plane (“y”) phase encode weighting (varied for each TRMP2RAGE), but with different 3D (“z”) phase encoding gradients (varied at each TR). The center of k-space for the 3D phase encoding direction is acquired at the TI for each GRE imaging block. The main motivation for developing the MP2RAGE pulse sequence was to provide a metric similar to MPRAGE, but with self-bias correction of the static (B0) and receive (B1-) magnetic fields, and a first order correction of the transmit magnetic field (B1+). However, because two images at different TIs are acquired (unlike MPRAGE, which only acquires data at a single TI), information about the T1 values can also be inferred, thus making it possible to generate quantitative T1 maps using this data.

Global feedback : good but repeating the paragraph highlighted above feels strange for the reader

[tomDag25]

Feedback for T1 Mapping -> MP2RAGE -> Benefits and Pitfalls

Global feedback : good

[tomDag25]

Feedback for T2 Mapping -> Introduction

Global feedback : good

[tomDag25]

Feedback for T2 Mapping -> T2 mapping vs T2-weighted imaging

Global feedback : good

[tomDag25]

Feedback for T2 Mapping -> Monoexponential T2 mapping -> Introduction

Global feedback : good

[tomDag25]

Feedback for T2 Mapping -> Monoexponential T2 mapping -> Signal modelling

Global feedback : good

[tomDag25]

Feedback for T2 Mapping -> Monoexponential T2 mapping -> Data fitting -> Data fitting

Global feedback : good

[tomDag25]

Feedback for T2 Mapping -> Monoexponential T2 mapping -> Data fitting -> T2*

• eq 3.4 is the same as eq 3.2 and I'm not sure that it is normal
• I'm not sure to understand this part : Until now, we have assumed that the transverse signal (Mxy) decays exponentially with the echo time divided by the T2 constant (see Eq. 3.3). However, in practice, other factors such as B0 inhomogeneities can cause a more rapid loss of the transverse signal; this results in a faster transverse decay, which is referred to as T2 relaxation (see Figure 3.1). The relation between T2 and T2 is described as follows Brown et al., 2014:

Global feedback : I don't know much about the subject but this part wasn't so clear to me

[tomDag25]

Feedback for T2 Mapping -> Monoexponential T2 mapping -> Data fitting -> Noise

Global feedback : Good

[tomDag25]

Feedback for T2 Mapping -> Monoexponential T2 mapping -> Benefits and Pitfalls

• MESE : only SE is highlighted

Global feedback : Good

[tomDag25]

Feedback for T2 Mapping -> Multiexponential T2 Mapping -> Introduction

Global feedback : Good

[tomDag25]

Feedback for T2 Mapping -> Multiexponential T2 Mapping -> Signal Modelling

• There is a figure 3.7 legend that doesn't exist : same text as the legend from fig 3.4. There is allready a fig 3.4 in Noise for monoexponential T2 mapping

Global feedback : Good

[tomDag25]

Feedback for T2 Mapping -> Multiexponential T2 Mapping -> Data Fitting

• According to the last feedback the number of the fig 3.5 is not the good one

Global feedback : Good

[tomDag25]

Feedback for T2 Mapping -> Multiexponential T2 Mapping -> Applications -> Myelin water fraction (MWF) imaging

Global feedback : Good

[tomDag25]

Feedback for T2 Mapping -> Multiexponential T2 Mapping -> Applications -> T2* and quantitative susceptibility mapping (QSM)

Global feedback : Good

[tomDag25]

Feedback for T2 Mapping -> Multiexponential T2 Mapping -> Applications -> Benefits and pitfalls of multi-exponential T2 mapping

Global feedback : Good but maybe I wouldn't put it in Applications so that it respects the organisation of the other sections

[mathieuboudreau]

Thanks a lot for the feedback @tomDag25 ! Just wondering if you think you were done providing feedback, or if you think you'll continue at a certain point. No pressure either way!

[tomDag25]

I was just waiting because you told me that the remaining chapters were maybe not mature enough but yes I will @mathieuboudreau !

[tomDag25]

Feedback for B1 mapping -> Double Angle Methods->transmit and receive RF field amplitudes

• "properties (electromagnetic permittivity ε and permeability μ) of the object being imaged" -> would put the parentheses at the end of the sentence

Global feedback : I didn't really get the explication of the distinction between B1+ and B1-, maybe a scheme could help

[tomDag25]

Feedback for B1 mapping -> Double Angle Methods -> Double Angle Methods

• typo: technique swherein
• typo: (Figure 4.1])

Global feedback: good

[tomDag25]

Feedback for B1 mapping -> Double Angle Methods -> Gradient echo and 180 degree spin echo method

• Alternatively, a gradient echo could be used? -> really a question ? If so maybe write it like that: Alternatively, could a gradient echo be used?
• typo: Assuming an an refocusing
• no latex ? Knowing that alpha = B1 alpha_nominal, B1

Global feedback: Maybe a text to describe what the reader should understand from the figures because I don't find it so intuitive. Else it's good !

[tomDag25]

Feedback for B1 mapping -> Double Angle Methods -> Appendix A

Feedback: nice proof but looks maybe a bit complicated for someone that doesn't do math... I don't know to what extent it's obvious that e^ix = cosx + isinx.
Other maybe easier ways to prove that is to compute the derivate of sin(2x)-2cos(x)sin(x), or basically use the identity: sin(a+b) = cos(a) sin(b) + sin(a) cos(b) ? However that's just a remark because I don't know if someone that doesn't like math would bother to read the proof.

[tomDag25]

Feedback for B1 mapping -> Actual Flip Angle Imaging -> Introduction

• change of formatting with: 1 Actual Flip Angle Imaging (AFI)
• Feels strange to come back in the introduction on a subject we are already talking about since a few chapters

Global feedback: this part feels a bit less integrated to the course (come back on things already discussed) and feels more like a paper introduction instead of a course. Else the content on AFI is good !

[tomDag25]

Feedback for B1 mapping -> Actual Flip Angle Imaging -> Signal Modelling

• Bloch equations -> maybe add a ref
• I feel like fig4.5 would be better placed if it was after the paragraph where it's cited

Global feedback: good

[tomDag25]

Feedback for B1 mapping -> Actual Flip Angle Imaging -> Data fitting

• Figure 4.10 doesn't display

Global feedback: good

[tomDag25]

Feedback for B1 mapping -> Actual Flip Angle Imaging -> Benefits and Pitfalls

• add for the whole AFI section the signification of AFI and DAM abbreviations

Global feedback: good

[tomDag25]

Feedback for B1 mapping -> Filtering -> Introduction

• Maxwell equations -> add a link ?
• no source: Sled and Pike 1998
• Figure 1 -> no such figure

Global feedback: good

[tomDag25]

Feedback for B1 mapping -> Filtering -> Filters and smoothing

• in the next section -> i think you can remove it
• eq 4.15: should be (fxg)(t) = ...
• eq 4.16: maybe put g and not f because in the previous paragraph "f(t) is the signal of interest and g(t) is the kernel"
• and is a measure of the width -> add sigma
• Figure 4.16: if you want to put Gaussian width I would still put sigma for those more familiar with gaussian functions
• add a link or an explanation for Fourier transform

Global feedback: good

[mathieuboudreau]

Thanks for all this recent feedback - yes the B1 section needs more polish, it's on a to-do list; thanks for catching a lot of these minor issues

[tomDag25]

Feedback for B1 mapping -> Filtering -> Filters and smoothing

• typo: help provide you with

Global feedback: good