PONE-D-21-01984

Machine learning to extract muscle fascicle length changes from dynamic ultrasound images in real-time

PLOS ONE

Dear Dr. Rosa,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Apr 08 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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We look forward to receiving your revised manuscript.

Kind regards,

Yih-Kuen Jan, PhD, University of Illinois at Urbana-Champaign

Academic Editor, PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: I Don't Know

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This paper aims to provide a benchmarking assessment of using several available machine learning programs to track soleus fascicle lengths during different functional movements, including calf raises and walking. The authors have made all data available and I believe this manuscript has broad impact in the fields of biomechanics and rehabilitation.

I do have a few comments for the authors to consider before final publication:

In lines 145-147 the authors mention that there was no movement of the heels or knees during constrained plantarflexion. However, it is extremely difficulty to provide a strong plantarflexor torque without movement in this position without the legs constrained (i.e. thighs fixed so knees cannot move). Was this the case? The images that show the different tasks don't look like this was the case. If so, please add.

In lines 197-199 - it is possible that I misinterpreted this analysis, but as lower RMSE would be better, I think there may be an error in your description on adding the inverse of RMSE (to make lower values better). Wouldn't inverting RMSE make higher numbers better since the usual RMSE would indicate lower is better? This is a bit confusing in this region so clarification would be appreciated.

Figure 4 - is the 7 seconds of data represented here standardized to the same portion of the gait cycle? Was RMSE/correlations different in various parts of the gait cycle? As indicated in the discussion, it would be expected if the correlations were higher during a portion of the gait cycle with less noise introduced by gait contact. Is this the case?

Reviewer #2: In this study, the authors have investigated the machine learning to extract muscle fascicle length changes from dynamic ultrasound images in real time. The topic of the manuscript is interesting. However, there are some minor concerns that should be addressed before the article can be accepted for publication.

1.Please describe the purpose of the study more specifically.

2.Please explain more about how the ultrasound images were obtained while the particitares rotate their ankle and walk task simultaneously?

3. In table 1 and 2, the parameter "CORR(r)" are calculated with other clinical data. Please describe how the values of "CORR(r)" are estimated with input data.

4.In table 2, what the possible reason for lower values of "CORR(r)" for cross-task training? And what's those values mean in the red color in table 1and 2?

5.It was mentioned six participants voluntarily participated in this experiment. Can the authors explain that the database is enough for training machine learning?

6.Which ML model is optimal by the results in this study?

Reviewer #3: The authors attempted to use machine learning (ML) models to record muscle fascicle lengths in real-time. The current result showed that the performance of support vector machine (SVM) model was the best with an acceptable r and RMSE, indicating that it is possible to track soleus muscle fascicle with ML models. However, there are still some issues that need to be clarified.

MAJOR COMMENT

Introduction

I was wondering why this study chose soleus as the target muscle. Could the authors explain why measuring soleus muscle fascicle length is important? For me, gastrocnemius may be more important than soleus in functional activities.

Methodology

First, how did you stabilize the ultrasound transducer on the muscle belly in performing dynamic tasks? There are various equipment or devices that stabilize the probe during dynamic movement in the past studies. Please elaborate this experimental setting in the method. Second, why did you ask participants to perform each movement in the same order? Did that affect the outcomes? Third, I did not understand the reason to select the last part of data as ground-truth rather than the random samples. Could you explain the explanation more? Why could this approach simulate the real-time measurement settings? Last, I did not understand how you calculated Pearson correlation coefficient. What 2 variables did you want to develop the correlation? How did you derive multiple r values to average them?

Results and Discussion

Could you separate the results from discussion? I still think it would be better to make 2 sections apart. In addition, I was curious why the SVM was the best model. Was there any possible reason?

MINOR COMMENT

Line 240: What does “moderately strong correlation” mean? I consider “moderate to strong” might be a better expression.

Line 383: “For example, it may be ‘that’ in…” What did “that” indicate in this sentence?

Line 404-406: “Furthermore, feeding ultrasound images…robustness and/or resolution.” Could you elaborate more why feeding data from other devices that assess muscle quality could improve the measurement robustness and resolution? In my opinion, these devices record different qualities of muscle, so they provide different information regarding muscle.

All tables: All tables need bottom border. And please put footnotes to explain CORR because r is not unit.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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PONE-D-21-01984R1

Machine learning to extract muscle fascicle length changes from dynamic ultrasound images in real-time

PLOS ONE

Dear Dr. Rosa,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by May 21 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Yih-Kuen Jan, PhD

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: (No Response)

Reviewer #2: Yes

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: (No Response)

Reviewer #2: Yes

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: (No Response)

Reviewer #2: Yes

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: (No Response)

Reviewer #2: Yes

Reviewer #3: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: By the responses form the authors, it may be found that the comments have been addressed appropriately.

Reviewer #3: For the issue regarding movement task order, like you said, strenuous tasks might influence the muscle fascicle lengths. Therefore, it might be a limitation in this study.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Machine learning to extract muscle fascicle length changes from dynamic ultrasound images in real-time

PONE-D-21-01984R2

Dear Dr. Rosa,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Yih-Kuen Jan, PhD, University of Illinois at Urbana-Champaign

Academic Editor, PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #3: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #3: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: (No Response)

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #3: No