PONE-D-19-27308

Micro-structure diffusion scalar measures from reduced MRI acquisitions

PLOS ONE

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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

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

Reviewer #1: Yes

Reviewer #2: Yes

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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

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Reviewer #1: Yes

Reviewer #2: 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: The purpose of this work is to present a method for the estimation of the microstructural scale, e.g. RTOP, RTPP, and RTAP from single-shell acquisitions. The paper presents a simplified formulation to calculate these scales with the assumption that the diffusion anisotropy is roughly independent of the radial direction. The proposed work proves its usability in the different acquisitions. The manuscript is concise and well explained and organized. I have a few comments on the manuscript:

1. "...assuming the diffusion anisotropy is roughly independent of the radial direction.", Please have an explaining of the rationality of this hypothesis for clinical applications. Also, what are the special requirements for the acquisition scheme?

2. Please also give some results to explain the impact of the number of gradient samples (or angular resolution) on the results.

3. Note that the experiment implemented in higher b-value on the result, e.g. Figure.1 and Table.3. What happened with b=1000?

4. Please clarify the definition of the correlation coefficient in Table.3.

5. In Figure.1, the RTPP calculated by AMURA seems to be significantly different from the results from other others. which is obviously cleaner. It seems to be related to the hypothesis that diffusion anisotropy is roughly independent of the radial direction. But it's still unclear whether this kind of change is an improvement. So it is better to show the correlation of RTPP with MD or RD.

Reviewer #2: In this paper, the authors propose a set of novel diffusion indices, called apparent measures using reduced acquisitions (AMURA), which can mimic the EPA-derived indices, but require only single-shell dMRI data. AMURA are based on the observation that EAP-derived indices are radial integrations of a set of measures at different shells. Based on this observation, the authors simplify the acquisition to a single-shell case and propose a set of single-shell measures to mimic EPA-derived indices, including RTOP, RTPP, and RTAP. The authors first show the analytical solutions for AMURA and then provide detailed numerical implementations by using spherical harmonics. AMURA is evaluated using a normal dataset, HCP, and a patient dataset, PPD. Three baseline methods, including RBF, MAPL, and MAP-MRI, are involved in the evaluation. Extensive experimental results demonstrate the effectiveness of AMURA, both qualitatively and quantitatively.

The paper is written well and motivation is clearly stated. AMURA are novel indices, which allow the study of brain disorders using EPA-like indices and clinical dMRI data. Regarding the proposed method, I have several minor concerns.

1. AMURA change at different b-values. Is there an optimal b-value for AMURA? For instance, which b-value gives the best AMURA that are most similar to the EAP-derived indices?

2. Page 10: A threshold is selected in the valley right after the main lobe in each case (for RTOP: 2 · 10^6 mm^−3 ; for RTPP: 90 mm^−1; for RTAP: 1.5 · 10^4 mm^−2 ). Please clarify whether all comparison methods share the same set of thresholds, or not.

3. The experimental results are convincing and sufficiently demonstrate the effectiveness of AMURA. However, I am wondering whether synthetic data experiments are useful or not since we do not have ground truth EAP measures in real data experiments.

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Reviewer #1: Yes: Ye Wu

Reviewer #2: No

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Micro-structure diffusion scalar measures from reduced MRI acquisitions

PONE-D-19-27308R1

Dear Dr. Tristán-Vega,

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

Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication.

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With kind regards,

Pew-Thian Yap

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 #1: All comments have been addressed

Reviewer #2: 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: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: 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: Yes

Reviewer #2: 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: Yes

Reviewer #2: 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: The authors have properly resolved all of my concerns and substantially improved the manuscript. So I would recommend its publication.

Reviewer #2: All comments have been well addressed in this revised version. I do not have any additional comments. This paper can be accepted.

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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: Yes: Ye Wu

Reviewer #2: No