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Welcome to the fNIRS FRESH project

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Robert Luke
Posts: 6
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(@rob_luke)
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Introduction

Thank you for participating in the fNIRS REproducibility Study Hub (FRESH) project. This project aims to explore the range of analysis techniques utilised by the fNIRS community and quantify the variation in conclusions drawn when many independent researchers analyse the same dataset.

Two datasets are provided as part of the FRESH study, and you should address the hypotheses for each dataset. You will need to state if your analysis supports each hypothesis or not. We will then ask you to fill out a free-form description of your analysis procedure. Once we have collected the responses from all participants, there will be a follow-up form to fill in that will ensure that we have collected the same information from all participants/teams.

 

Instructions

  • Register for the project (description below).
  • Download the data (described below).
  • Use the data to test each hypothesis (described below).
  • Report your response to each hypothesis using this form.
  • Once we have collected all responses, we will reach out again and ask you to fill out a detailed questionnaire about your analysis procedure.

 

Expectations

  • Teams must submit their results within the prescribed time frame (4 months).
  • Multiple teams from the same institution may register for the project.
  • You can register as an independent, you do not need to be part of an academic institution.
  • Teams may consist of one or more individual participants.
  • There must be a significant contribution from each member of the team.
  • This is not a competition. We will not be ranking the performance of participants. The paper will not link the authors/teams to specific results.
  • Do not discuss your analysis approach, strategy, or outcomes with other teams.
  • You attempt to address all hypotheses. However, if your usual analysis approach does not allow you to answer certain questions, you can skip them and note this in your response.
  • You may use the https://openfnirs.org/community forum to discuss practical issues such as loading data.
  • All participants must professionally conduct themselves and be considerate to other participants and the coordinating team.

 

Registration

To register for this study please complete these steps:

  1. Add your institution if it is not in the list below using this form. (you do not need to be part of an institution, you can register as an independent)
  2. Add each participant using this form
  3. Register your team using this form.  (A team can be a single participant or have many people in the team)

Once you have completed these steps we will send you a confirmation email in the following weeks. You can modify your team and individual details at any time. We will reconfirm each team after you submit your results.

Registering does not oblige you to commit to entering the study. It just allows us to contact you and provide you with further information as it becomes available. You can remove yourself at any time.

 

Timeline

Due to the scale of this project, a strict timeline will be adhered to. Participants will have 4 months to analyse the data and submit their results.

  • October 3rd 2022: Data is released and result submission opens.
  • February 3rd 2023: Result submission closes.

 

Data

You can download the datasets from OSF at https://osf.io/b4wck/ .

The data is stored in SNIRF format and organised according to BIDS.

 

Research Questions

A set of hypotheses are listed below that you must address. The first dataset provides a set of group-level hypotheses, and the second dataset provides a set of individual-level hypotheses.

1. Auditory Dataset

Please address the following hypotheses at a group level.

Hypotheses

  1. Speech stimuli evoke responses in the left Heschl's gyri (HG).
  2. Speech stimuli evoke larger responses in the left HG than the noise stimuli.
  3. Speech evoked responses are larger in the left HG than the right HG.
  4. Speech evokes responses in the left inferior frontal gyrus (LIFG).
  5. Speech evokes a larger response in the LIFG than noise.
  6. Speech evokes responses in the occipital cortex.
  7. The silence condition evokes a response in the occipital cortex.

2. Motor Dataset

Please address the following hypotheses at the individual level. For each hypothesis, you will need to provide a response per participant.

Hypotheses

  1. Left hand finger tapping of 2 sec duration evokes a response in the contralateral primary motor cortex.
  2. Left AND right hand finger tapping of 2 sec duration, conditions combined, evokes a response in the contralateral primary motor cortex.
  3. Left AND right hand finger tapping of 2 AND 3 sec duration, conditions combined, evokes a response in the contralateral primary motor cortex.
  4. Left AND right hand finger tapping of 3 sec duration, conditions combined, evokes a greater response in the contralateral primary motor cortex than left AND right hand finger tapping of 2 sec duration, conditions combined.

Exploratory Analysis from the motor dataset

  1. Which brain regions (if any) differ in response to left and right finger tapping?

 

Dataset Information

Two datasets are provided with the FRESH study.

1. Auditory Dataset

Overview

This dataset is from "Analysis methods for measuring passive auditory fNIRS responses generated by a block-design paradigm" (Luke et al. 2021).

Preparation

Data were originally acquired using a NIRx NIRScout device and exported in native NIRx format. The data were then converted to BIDS format using the fNIRS-App sourcedata2bids using version 0.4.4.

2. Motor Dataset

Overview

The dataset contains NIRS data of 10 healthy, right-handed adults under different sensorimotor stimulation conditions. Each subject was required to perform a total of four sessions of a block-designed protocol: (1) 2 s right-hand finger tapping, (2) 3 s right-hand finger tapping, (3) 2 s left-hand finger tapping, and (4) 3 s left-hand finger tapping. The task blocks were interleaved with a rest period that varied between 10 and 20 s in all sessions. The optical probe contained 14 sources and 32 detectors, allowing 64 source-detector combinations (i.e., channels) at approximately 3 cm and four source-detector pairs (short channels) at 0.8 cm. The details of the probe setup and fNIRS acquisition are the same published in Novi et al. 2020.

Preparation

Data were originally acquired using a NIRx NIRScout device at 8.9 Hz and exported in NIRx format but without the probe info file. A probe info file was then manually generated. The data was converted to BIDS format using MNE-BIDS version 0.10.

General Information

  • The SNIRF files were validated using pysnirf2 version 0.7.4.

 

Frequently Asked Questions

  • The composition of my team has changed. What should I do?
    • You can register a new team (this is the preferred option) or email the details to committee@fresh-fnirs.org, and we will update our notes. We will also ask everyone to confirm their team and members in the final questionnaire.
  • My analysis procedure was different for each hypothesis. How can I report this?
    • You can include as much detail as you wish in the initial free-form response. If you have used different analysis approaches, then please describe each analysis in complete detail and indicate which question it was used to address.
  • Where do you plan to publish these results?
    • We are aiming to publish this article in Neurophotonics. This journal does not have a limit on the maximum number of manuscript authors.
  • Will all team members be listed as authors on the final publication?
    • In the final questionnaire, you will be asked to describe the contribution of each team member and if you consider their contribution to be substantial enough to warrant co-authorship. Some journals have a policy on the number of authors on a paper. So we can not guarantee all team members will be included as co-authors. At a minimum, we will ensure that the lead from each team is included as an author.
  • The analysis procedures used in your lab do not allow you to answer a specific question.
    • You are not required to answer all of the questions. You can select "Not investigated".
  • I am unable to open the files using software {your favorite software}.
    • Please inform us using the openfnirs forum and we will try and resolve this with you.
  • I found a mistake. Something is ambiguous.
    • Please inform us using the openfnirs forum and we will try and resolve this with you.

 

Regards,

Rob, Rickson, Meryem

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Robert Luke
Posts: 6
Topic starter
(@rob_luke)
Active Member
Joined: 1 year ago

Please ensure you are using the latest version of your analysis software package.

For Homer users this is version v1.52.0 https://openfnirs.org/community/postid/1346/ https://github.com/BUNPC/Homer3/releases

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Meryem Yücel
Posts: 133
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(@mayucel)
Estimable Member
Joined: 2 years ago

The Homer release compatible with BIDS & snirf: v1.54, to download

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