PONE-D-23-03044Non-Cartesian 3D-SPARKLING vs Cartesian 3D-EPI encoding schemes for functional Magnetic Resonance Imaging at 7 TeslaPLOS ONE

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Sumit Datta, PhD

Academic Editor

PLOS ONE

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Additional Editor Comments:

We have received two expert reviews. However, both reviewers raise many critical issues. After carefully reading this work, I have to agree with the reviewers that the significance of this work is marginal. So, I recommendation a major revision of the your manuscript.

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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: Partly

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: No

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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: No

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Reviewer #1: No

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 paper is generally well written and structured but I suggest minor re-.

The literature review was

thorough, It is comprehensive and

completely justifies

No technical errors and approved for publication

Reviewer #2: In this paper, a 3D-SPARKLING trajectory is evaluated for use in whole-brain isotropic functional MRI at 7 T. The proposed method uses a non-Cartesian readout, coupled with a non-linear reconstruction (compressed sensing with wavelet domain sparsity), and was compared to conventional 3D-EPI with matched parameters. While image quality in the 3D-SPARKLING acquisition was poorer than the 3D-EPI, most metrics showed improved sensitivity and specificty for the proposed method over 3D EPI, evaluated in 6 healthy volunteers.

The paper is reasonably well written, and many comprehensive experiments/evaluations are performed. However, I have several reservations about the results presented in the paper:

Major Comments:

1. The paper doesn't provide a figure or diagram of the resulting 3D SPARKLING trajectory. However, my understanding is that 3D SPARKLING optimized trajectories depend heavily on initialization, and in previous work, 3D SPARKLING trajectories were initialized with perturbed 3D radial trajectories. One would assume this to be the case here as well (although it is unstated as far as I can tell). Given this, it is quite confusing that the 3D-SPARKLING trajectories is stated to have been acquired in the "P-A encoding direction" (see Line 163). This is also stated in the bottom row of Table 1. It would be useful for the authors to explain in what way exactly the "P-A encoding direction" is meaningful in the context of 3D SPARKLING.

2. It is somewhat difficult to believe that despite poorer image quality, 3D-SPARKLING outperforms 3D-EPI in nearly every quantitative metric. As the BOLD signal is encoded in the image magnitude, one might expect that the blurring/aliasing seen in the image should also be reflected in the BOLD signals. The authors address this point in part by appealing to BOLD PSFs, but if it is expected that inclusion of dynamic off-resonance correction would significantly improve image quality, I believe the manuscript would significantly benefit from including that, rather than leaving it for future work. It would be difficult to recommend a method that produces qualitatively worse looking images, despite what the quantitative metrics show.

3. Another reasons CS has not been widely adopted in fMRI is due to the nonlinear reconstruction. In contrast with most linear reconstructions (e.g. parallel imaging), CS reconstructions are not unbiased, and furthermore, due to the non-linearity of the reconstruction, characteristics of the resulting "noise" is not straightforward. As most fMRI analysis tools have assumptions grounded in the Gaussianity of residuals, while this can be true for linear reconstructions (in the high SNR limit anyway when dealing with magnitude images), no guarantees about the distributional properties of the signal residuals can be made with CS reconstructions. This may be confounded further by interaction with image pre-processing. Therefore, naive adoption of fMRI analysis methods without consideration of altered noise characteristics is statistically unsound. At a minimum, some validation of the residual characteristics of the fMRI analysis models would help establish their statistical validity. Discussion of this important point should also be included in the manuscript. Although the reconstructions performed here are done independently volume-to-volume, if time-dependent regularization is performed, then additional considerations of any potential loss of temporal degrees of freedom are also necessary to ensure statistical validity of the inference process.

4. As a followup to point 3, evaluation of tSNR is not particularly meaningful when comparing biased (CS) vs. unbiased (PI) reconstructions. Between unbiased reconstructions, tSNR evaluation is appropriate as it is related to mean squared error (no bias). However, heavily regularized CS reconstructions could potentially have infinite tSNR, as variance is reduced to zero (as tSNR does not penalize bias). Therefore, some consideration of this fact should be taken into account when reporting tSNR.

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Reviewer #2: No

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PONE-D-23-03044R1Non-Cartesian 3D-SPARKLING vs Cartesian 3D-EPI encoding schemes for functional Magnetic Resonance Imaging at 7 TeslaPLOS ONE

Dear Dr. Amor,

Thank you for submitting your manuscript to PLOS ONE.   As suggested by the reviewer, authors are requested to recheck and correct the typographical or grammatical mistakes if any. Therefore, we invite you to submit a revised version of the manuscript.

Please submit your revised manuscript by Nov 16 2023 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: https://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,

Sumit Datta, PhD

Academic Editor

PLOS ONE

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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.

Additional Editor Comments:

Authors address all the queries resaid by reviewers. As suggested by the reviewer, authors are requested to recheck and correct the typographical or grammatical mistakes if any.

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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

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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

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

Reviewer #1: (No Response)

Reviewer #2: Yes

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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: No

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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

Reviewer #2: Yes

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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: I require authors to make some minor revisions

article must be clear and correct, some typographical errors must be corrected.

Also some grammatical errors should be corrected.

Reviewer #2: (No Response)

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Reviewer #1: No

Reviewer #2: No

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Non-Cartesian 3D-SPARKLING vs Cartesian 3D-EPI encoding schemes for functional Magnetic Resonance Imaging at 7 Tesla

PONE-D-23-03044R2

Dear Dr. Amor,

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.

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Kind regards,

Ozlem Ipek, Ph.D.

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: (No Response)

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: (No Response)

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

Reviewer #1: Yes

Reviewer #2: (No Response)

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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: (No Response)

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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: (No Response)

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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: (No Response)

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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

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