---
title: hMRI Meeting Sept. 2019
tags: hMRI
---

[TOC]

hMRI Meeting Sept. 2019
===

###### tags: `hMRI` `Meeting`

:::info
- **Location:** WIAS Berlin, Mohrenstraße 39, 10117 Berlin [https://www.openstreetmap.org/node/5374911183]
- **Date:** Sept 4, 2019, 10:00 - Sept 5, 16:00
- **Participants:**
- Gunther Helms
- Nikolaus Weiskopf
- Christophe Phillips
- Evelyne Balteau
- Siawoosh Mohammadi
- Antoine Lutti
- Ferah Kherif
- Enrico Reimer
- Gabriel Ziegler
- Martina F. Callaghan
- Karsten Tabelow
- **Contact:** Karsten Tabelow <[e-mail]>

:::

---

# Practicalities

## Local accommodation
* [Motel One Spittelmarkt](https://www.motel-one.com/de/hotels/berlin/hotel-berlin-spittelmarkt/)
* [Novotel Berlin Mitte](http://novotel-berlin-mitte.hotel-in-berlin.org/de/)
* [Best Western Am Spittelmarkt](http://book.bestwestern.com/bestwestern/DE/Berlin-hotels/BEST-WESTERN-Hotel-am-Spittelmarkt/Hotel-Overview.do?propertyCode=95382&srcPage=SelectHotel&isMapOpen=true&selectedHotels=)
* [Titanic Comfort Berlin](http://www.titanic.com.tr/titaniccomfortmitte/default-de.html)

## Transport

* Closest train/metro station: [U2 Hausvogteiplatz](https://www.bvg.de)
* Estimated time Berlin Hbf.-Hausvogteiplatz 15 minutes by bus/metro
* Estimated time Berlin Hbf.-Hausvogteiplatz 35 minutes walking
* Estimated time Berlin SXF-Hausvogteiplatz 50 minutes by train (Ticket ABC)
* Estimated time Berlin SXF-Hausvogteiplatz 45 minutes by taxi
* Estimated time Berlin TXL-Hausvogteiplatz 40 minutes by train (Ticket AB)
* Estimated time Berlin TXL-Hausvogteiplatz 35 minutes by taxi

# Timetable

## September, 4th

| Time | Topic |
| --- | --- |
| 10:00 | Introduction |
| 10:15 | Software engineering/quality/unit test (**Nik Weiskopf**)|
| 11:15 | state of affairs (status quo/issues/future work) part 1 (**Antoine Lutti**)|
| | - Weierstrass goes MRI: The general algebraic framework behind the toolbox (GH) 30mins|
| | - R2s* higher-order model (SM) |
| | - Adaptive smoothing (MFC) |
| | - RF spoiling calculations (MFC) |
| | - MPM Reliability Study and Scanner Effects (GZ) |
| | - hMRI usage from multiple platforms/vendors (GH) |
| 12:15 | *Lunch* at [Lunch Time](https://goo.gl/maps/U4vsV777vHnAcmtz8) |
| 13:15 | state of affairs (status quo/issues/future work) part 2 (**Antoine Lutti**) |
||Clinical applications (FK): |
||- Validity & utility in paradigmatic brain pathologies
||- Longitudinal data - from preprocessing to analysis & interpretation|
||- Suite for default uni-/multivariate analysis of MPM data|
| 15:15 | *Coffee* |
| 15:45 | state of affairs (status quo/issues/future work) part 3 (**Christophe Phillips**), spatial processing |
| | - implicit and explicit masking. [Recent issues and fixes](https://github.molgen.mpg.de/cphillips/hMRI-toolbox-processing/issues/1).|
| | - switching from DARTEL to SHOOT for improved normalization? |
| | - BIDS and the hMRI toolbox. How to fit in the international effort, advantages and constraints. See the [BEP001 ongoing work](https://docs.google.com/document/d/1QwfHyBzOyFWOLO4u_kkojLpUhW0-4_M7Ubafu9Gf4Gg/edit#heading=h.6e5avk8akeqj) |
| | - making more datasets and publicly available? Not just a single subject but the whole group(s) with raw data (BIDSified and anonimized ideally) and maybe the generated quantitative maps |
| | - integration of the brainstem segmentation tool by Christian Lambert, see [reference](https://doi.org/10.1016/j.nicl.2013.04.017) and his [project on qMRI](http://qmaplab.com/). |
| 17:45 | Management/Organisation & Wrap up (**Karsten Tabelow**)|
| 19:00 | *End of day 1* |
| 19:00| Dinner at [Good Time](http://www.goodtime-berlin.de/) (Thai food at Hausvogteiplatz)|

## September, 5th

| Time | Topic |
| --- | --- |
| 09:00 | Catch up from D1 (**Karsten Tabelow**)|
| 11:00 | Future developments (**Siawoosh Mohammadi**)|
| | - errormaps (SM) |
| | - g-ratio (SM) |
| | - quality measures extracted from the MPM data (AL) |
| | - hMRI group (SM/KT/EB) |
| 12:00 | *Lunch* |
| 13:00 | Grant planning & external collaborators (**Martina Callaghan/Siawoosh Mohammadi**/KT:NS??)|
| 14:00 | Wrap up |
| 15:00 | *End of meeting* |
| 15:00 | Presentation by Graham Cooper, Stefan (Paul) Koch, Philipp Böhm-Sturm on hMRI for mouse studies |
| 16:00 | *End of add-on* |

---

# Meeting results

## Action points following meeting

~~ER - delete VBQ-toolbox-group from github.molgen to remove reference to the defunct repository~~
ER - (re)discuss code/repository structure
ER - find CI platform
ER - get wiki to private
ER - check matlab function tests https://www.mathworks.com/help/matlab/matlab_prog/write-function-based-unit-tests-.html
ER - look for the release file
KT - explore use of existing code, as an independent function, to extend R1 fitting to incorporate multiple flip angles and remove linear approximations. Feedback recommendations for implementation requirements to map creation group.
MFC - implement utility function for imperfect spoiling correction.
MFC - arrange t-con between KT and adaptive smoothing developers at the FIL.
CP - liaise with Chris Lambert re integration of brainstem and sub-cortical analyses methods into toolbox within spatial processing group.
ER, CP, EB - develop framework for marking code as experimental.
ER - investigate what has gone wrong with automatic creation of git version file.
All - check if there are any additional datasets at your site that could be made publicly available.

## Next meeting
- Beginning of September (week of 7th or 14th) in Liege or in Hamburg by SM - CP is sending an email.
- Workshop organized by CP & EB or SM + hMRI team;
- Training Course: Physics to application
- what are data
- basic creation
- calibration
- spatial processing:
- segmentation with new probability maps & normalisation
- VBQ smoothing
- statistical analyses & inference
- [OHBM](https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3940) Educational Course in Montreal, -> rather go for a Symposium!
- tentative title "Quantitative MRI, from physics to application."
- meeting is on June 25-29, 2020, but course should be on the *last* day (unlike previous editions). TBC.
- submission opens on September 16, deadline December 19.
- need for diversity: sub-topics, labs, tools & **gender**
- Scientific Workshop: Nikola Stikov / Tobias Auer / Aviv Mezer / Tobias Wood / [Gilles de Hollander](https://scholar.google.com/citations?user=vFqZH9kAAAAJ&hl=nl) &#8594; for the OHBM educational course?

## Working Group - short

- [x] Software engineering (NW) [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/oBRDTBexJbrc4Tm)
- [x] Weierstrass goes MRI: The general algebraic framework behind the toolbox (GH, KT, SM) [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/esYPaSoDsHEKZTR)
- [x] R2s* higher-order model (SM, KT, NW, FK) [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/Xtwc8ySPKgx6gSk)
- [x] Adaptive smoothing (KT, MFC, SM, NW) noSlides
- [x] RF spoiling calculations (MFC) noSlides
- [x] MPM Reliability Study and Scanner Effects (GZ, NW, FK, GH, SM, MFC) [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/Js8NNc2e9reTqDY)
- [x] hMRI usage from multiple platforms/vendors (NW, GH) [Slides/NW](https://cloud.wias-berlin.de/aotearoa/index.php/s/8rzTFsgSKDi8aMX) & [Slides/GH](https://cloud.wias-berlin.de/aotearoa/index.php/s/esYPaSoDsHEKZTR) - DONE!
- [x] Clinical applications (FK): [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/mKaQDggt3ZQHfjW)
- Validity & utility in paradigmatic brain pathologies (service by FK)
- Longitudinal data - from preprocessing to analysis & interpretation (FK, BD, CP, GZ)
- Suite for default uni-/multivariate analysis of MPM data (FK, BD, CP, GZ, MFC)
- [x] implicit and explicit masking. (CP) [Recent issues and fixes](https://github.molgen.mpg.de/cphillips/hMRI-toolbox-processing/issues/1). [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/qaSe77cTdYj7QAd)
- [x] switching from DARTEL to SHOOT for improved normalization? [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/qaSe77cTdYj7QAd) (CP, CL) - FOR FUTURE!
- [x] BIDS and the hMRI toolbox. How to fit in the international effort, advantages and constraints. See the [BEP001 ongoing work](https://docs.google.com/document/d/1QwfHyBzOyFWOLO4u_kkojLpUhW0-4_M7Ubafu9Gf4Gg/edit#heading=h.6e5avk8akeqj). (CP, TL, DR) [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/qaSe77cTdYj7QAd)
- [x] making more datasets and publicly available? Not just a single subject but the whole group(s) with raw data (BIDSified and anonymized ideally) and maybe the generated quantitative maps (CP)
- [x] integration of the brainstem segmentation tool by Christian Lambert, see [reference](https://doi.org/10.1016/j.nicl.2013.04.017) and his [project on qMRI](http://qmaplab.com/). [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/qaSe77cTdYj7QAd)(CP)
- [x] errormaps/quality measures (SM, KT, AL, MFC) [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/8tyWEibHRA5HC77)
- [x] g-ratio (SM, NW, MFC) noSlides, noPresentation
- [x] Stats using confidence intervals / outlier-info (AL, FK, CP, GZ, KT) [Slides](https://cloud.wias-berlin.de/aotearoa/index.php/s/6Az536TY3WP3G7C)
- [ ] hMRI group (SM/KT/EB)

## Working groups

### Guidelines for Working groups

- self-organizing project groups
- one coordinator is defined
- integrate changes into experimental release version as early as possible; it does not have to be perfect
- [unit and integration testing](http://softwaretestingfundamentals.com/unit-testing/) must be performed
- experimental release version for developers lowers threshold for early and fast integration

### Dealing with pull requests

- EB, KT, CP

### Imperfect spoiling correction

- Resp: Martina
- Members/tasks: who want to take part and what for?
- TODOS
- schedule meeting time?
- pull request to private common repository
- GUI interface
- test function(s)

### R2* higher-order model

- Resp: SM
- Members/tasks: SM, KT, NW, FK
- Goal: ISMRM abstract with in-vivo data @7T (Peter Mccolgan's data?)
- TODOS
- add R2* fitting to my fork of the toolbox
- >Questions: 1) Can I combine both, error map generation and R2* higher order fit into my fork or should they be on different branches? 2) How do I ensure that my fork/branch is private? I think that the error map generation that I added to the hMRI toolbox is accessible to everbody
- pull request to private common repository
- GUI interface - don't need to change anything
- test function(s)

### Error maps, QC & outliers identification

- Resp:
- Members/tasks: who want to take part and what for? -> Siawoosh, Antoine, Martina, Nik, Gabriel?
- TODOS
- schedule meeting time
- pull request to private common repository (assuming it is something that would eventually come handy as QC tool for users)
- GUI interface
- test function(s)

### SDR2* maps etc...

- Resp: Antoine
- Members: linked to WG juste above (Error maps etc) -> Karsten, Gabriel, Martina...?
- TODOS
- schedule meeting time
- pull request to private common repository (assuming it is something that would eventually come handy as QC tool for users)
- GUI interface
- test function(s)

### Noise and adaptive smoothing

- Resp:
- Members/tasks: who want to take part and what for? Martina, Siawoosh, Karsten
- TODOS
- schedule meeting time
- pull request to private common repository
- GUI interface
- test function(s)

### Weierstrass model & refactoring MTprot

- Resp: KT or GH?
- Goal: ISMRM abstract
- Members/tasks: KT/GH/SM - Evelyne?
- TODOS
- acquire multi-flip-angle data (GH & SM need to talk / coordinate about data acquisition)
- pull request to private common repository (KT)
- GUI interface (KT)
- test function(s)

### R1 estimate without linear approxiamtion

- Resp: Karsten
- Members/tasks: who want to take part and what for?
- TODOS
- schedule meeting time
- pull request to private common repository
- GUI interface
- test function(s)

### Brainstem and sub-cortical structures

- Resp: Chris
- Members/tasks: who want to take part and what for?
- TODOS
- liaise with Chris Lambert -> integration into hMRI?
- pull request to private common repository
- GUI interface
- test function(s)

### Repository organisation

- Resp: Enrico
- Members/tasks: who want to take part and what for? Chris, Evelyne
- TODOS
- schedule meeting time
- define workflow for experimental / public parts of the toolbox
- output "how to" procedure and guidelines for all new modules and features

### Reliability, reproducibility, scanner effect

- Resp: Gabriel
- Members/tasks: who want to take part and what for?
- TODOS
- schedule meeting time

### PD calculation

- Resp: Siawoosh
- Members/tasks: who want to take part and what for? Gunther, Antoine, Ferath, Tobias?, (Martina)
- Questions to be addressed (to be further discussed at first meeting)
- WM vs CSF calibration
- test and assess every step of the pipeline
- bias field effect? imperfect spoiling effect?
- look into literature, patients, aging, ...
- TODOS
- schedule meeting time
- pull request to private common repository
- GUI interface
- test function(s)

### g-ratio

- Resp: Siawoosh
- Members/tasks: who want to take part and what for? Martina, Nik, Antoine
- TODOS
- schedule meeting time
- pull request to private common repository (assuming it is something that would eventually come handy as QC tool for users)
- GUI interface
- test function(s)

# Appendix

## Topic suggestions before the meeting

### Overall topics
- toolbox management & organisation
- data conversion & organisation (+sharing?)
- map creation
- map processing
- eine kleine wiederholung der git-befehle machen
- mail base / anfragen bisher zusammenfassen
- strategie, wie wir die toolbox in zukunft pflegen wollen / neues einbauen wollen vorschlagne
- zukünftige features, die eingebaut werden sollen/könnten besprechen (hier könnten auch potentiell neue leute dazu kommen: mouse/bruker)
- in die runde fragen ob interesse besteht dass wir ein satelite meeting addieren um hmri toolbox zu vermarkten?

### Gunther Helms:

- multiple flip angles This becomes important for bias reduction at UHF.. My PhD student Hampus is currently working on it.
- B1(+) correction for MT: Much belated, I have finally submitted it to MRM as a note. However, the correction needs to be generalized beyond the current model. This is to cope with the vendors' implemented MT pulses. Based on preliminary data, I am fairly confident it can be done.
- bSSPF/TruFi/Despot2 follows the same algebra as FLASH, so we might consider implementing it in some future. As mentioned, I'd happily present a talk on "The Weierstrass substitution and the algebraic framework behind the hMRI toolbox"

### Christophe Phillips

- implicit and explicit masking. [Recent issues and fixes](https://github.molgen.mpg.de/cphillips/hMRI-toolbox-processing/issues/1).
- BIDS and the hMRI toolbox. How to fit in the international effort, advantages and constraints. See the [BEP001 ongoing work](https://docs.google.com/document/d/1QwfHyBzOyFWOLO4u_kkojLpUhW0-4_M7Ubafu9Gf4Gg/edit#heading=h.6e5avk8akeqj).
- integration of the brainstem segmentation tool by Christian Lambert, see [reference](https://doi.org/10.1016/j.nicl.2013.04.017) and his [project on qMRI](http://qmaplab.com/).
- switching from DARTEL to SHOOT for improved normalization
- setting up a Marie Curie ITN among the different contributors to the hMRI toolbox.
- making more datasets and publicly available. Not just a single subject but the whole group(s) with raw data (BIDSified and anonimized ideally) and maybe the generated quantitative maps.

Sessions could possibly be dedicated to discussion on similar topics, e.g. map creation, map processing, general code organization, future developments,...

### Nikolaus Weiskopf

I think it would be good to discuss how we bring in more developers, proper systematic testing and new features.

### Antoine Lutti

Following up on this email, the guy who is conducting this impressive MPM mouse work is Steve Sawiak from the Wolfson Brain Imaging Centre in Cambridge. His email address is: [e-mail]
He is the person behind SPMMouse, the SPM toolbox for mice data
He's done some really impressive work I think (see attached) he would be the right person to ask for help

That would definitely be a great addition I think - he seems very good judging from his output although I don't know him personally.
We could invite him to our group meeting that we're planning for september as an introduction. What do you guys think?

### Karsten Tabelow

- Spatially Adaptive Smoothing MPM data
- Correction for Rician (non-central Chi) bias
- Confidence intervals for qMRI estimates