Peer Review History
| Original SubmissionMay 16, 2024 |
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PONE-D-24-19418A novel mean shape based post-processing method for enhancing deep learning lower-limb muscle segmentation accuracyPLOS ONE Dear Dr. Guo, 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 Jul 26 2024 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:
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This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ 8. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [Note: HTML markup is below. Please do not edit.] 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 ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: I Don't Know ********** 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 ********** 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 ********** 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 study introduces a new post-processing method that compensates for the shortcomings of UNet-based segmentation methods based on Magnetic Resonance Imaging (MRI) scans and verifies its effectiveness in practice. The proposed method takes into consideration the muscle anatomical shape, enabling more effective and accurate segmentation of muscles. I believe that it is useful as it can be applied to other organ segmentation such as bone, lung etc. By comparing with existing post-processing approaches as well as a commercial segmentation software, it has demonstrated the good performance of the proposed post-processing approach. The paper is very well organised and written. Comments are: 1. The contribution of the study should be highlighted. 2. Obviously, the proposed post-processing approach can be apply in any segmented images. There are many different types of deep learning networks, can you explain why UNet was chosen as the deep learning model for this study? 3. In Participants, it looks like you used two different MRI scanners, were there any differences in imaging conditions between the two cohorts? 4. For the operators for manual segmentation, were they the same people or different people with similar technical level? 5. For the training, one cohort of data (PMW-1) was used as training data while the second cohort was used for test. Is there any population bias in the cohort which may affect your result? 6. In the proposed method, mean shape of the cohort (postmenopausal women) was used. What is your view for the method to apply to different population, say young people? Reviewer #2: The manuscript presents a new post-processing method for the automatic segmentation of muscles in the upper leg. I find the approach to use a mean shape quite interesting. Overall the manuscript is well-written and has scientific merit. I do have some comments that I hope the authors can help clarify. Comments are (largely) listed in order of appearance in the manuscript: General: When data is pooled, is this done after the predictions? Or is a separate U-Net trained for the pooled data. If only 1 label is available for training the U-Net I imagine that you could achieve much better results compared to only pooling in post-processing. Introduction: Just reading the introduction, the goals of the study slightly confuse me. In L91 you mention that a new SSM-based post-processing method is proposed in this study. However, in the subsequent paragraph, you say that the goal of the study is to assess the effect of existing post-processing methods, with no mention of the proposed novel method. From the rest of the paper it is clear that this SSM-based method is an essential part of the goal of this study. Methods: More information regarding the MR images should be presented (pixel size, slice thickness, slice increment, FOV, any filtering applied) L112-L124: it is unclear to me if the segmentations of PMW-1 were performed as part of this study, or in another study (reference 19). If I understand correctly, the scans for PMW-2 were segmented for this specific study. Were exactly the same muscles extracted? How was the segmentation performed? Was this also performed semi-automatically and performed by multiple operators and then compared? I believe that these segmentations are considered the golden standard mentioned in the results. I suggest mentioning this explicitly for clarity. I suggest trying to put table 2 into a flowchart figure as is often done with U-Net networks. L131: I'm a bit confused regarding how the U-Net was trained. Why was the U-Net trained and tested 3 times? Was it retrained for each method of post-processing? If so, wouldn't it make more sense to perform the post-processing on one trained model? Was there no validation set? What hyper-parameter settings were used? L141: I don't understand how muscles were 'manually selected using thresholding'. Section 2.5, fig 3.: Why were the initial U-Net predictions used to build the SSM? I believe that it would be better to use the original gold standard semi-automatic segmentations would lead to more accurate mean shapes. Now you are already limited by how good the initial U-Net predictions are. If this is not a mistake in writing, I believe this is quite crucial and requires more explanation. L273: In other publications I have seen the RVE presented as an absolute value. Was it a conscious decision to not use the absolute volume difference? Results: L326: I fail to see how the Hausdorff distance becomes meaningless with larger objects. Yes the HD will likely increase compared to the analysis of the individual muscles, but it can still be used to compare the various post-processing methods, no? Fig 7. I like this figure, but it's difficult to distinguish muscles where adjacent muscles are all colored dark blue. Discussion: Figure 10 and table 4 present results and thus fit better in the results section. L460: 'General consistency between the cohorts' does not appear true to me. There may not be a statistical difference, but I can imagine that there is a difference in muscles between subjects with a BMI of 26.5 +- 3.4 and 22.0 +- 2.1. Did you check the difference in volume, shape, etc. between the muscles in PMW1 and PMW2? It would be interesting to read your opinion on the generalizability of the MS post-processing method. It appears to me that you're confronted with quite a lot of smoothing when using a mean shape and this doesn't change when adding more subjects. Does this make this method only applicable for healthy, near-average subjects? Reviewer #3: In this manuscript, authors present a new mean-shape based post-processing method in order to improve the automatic muscle segmentation accuracy through deep learning models, more specifically, UNet. The study is interesting and important because although there are many deep learning structures and algorithms having been proposed for the purpose of automatic image segmentation, these algorithms often lack sensitivity to details which hinders satisfactory semantic segmentation results. Post-processing is a good way to improve or enhance the segmentation accuracy. 1. The paper is very well organised and written. English may be improved. 2. You have compared your method with Mimics commercial semi-automatic muscle segmentation toolbox. What is the main purpose of this comparison? Does Mimic have post-processing? 3. There are lots of deep learning algorithms for image segmentation, why UNet? 4. In your comparison, Mimics has lower RVE, which is better than your method. Any consideration for future improvement of your algorithm? 5. It looks like mean shape is the mean value of this specific cohort. What about other cohort? ********** 6. 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". 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| Revision 1 |
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A novel mean shape based post-processing method for enhancing deep learning lower-limb muscle segmentation accuracy PONE-D-24-19418R1 Dear Prof. Guo, 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. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. 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, Fei Yan 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 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 #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: No 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: (No Response) 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 #1: Yes: Quanmin Zhu Reviewer #2: No Reviewer #3: No ********** |
| Formally Accepted |
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PONE-D-24-19418R1 PLOS ONE Dear Dr. Guo, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Fei Yan Academic Editor PLOS ONE |
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