Peer Review History
| Original SubmissionJanuary 22, 2025 |
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Dear Dr. Shultz, 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 24 2025 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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Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. 3. Please include your full ethics statement in the ‘Methods’ section of your manuscript file. In your statement, please include the full name of the IRB or ethics committee who approved or waived your study, as well as whether or not you obtained informed written or verbal consent. If consent was waived for your study, please include this information in your statement as well. 4. 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. 5. 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 If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references.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 If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [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? Reviewer #1: Yes Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #2: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: Yes ********** Reviewer #1: In this piece of work, Kuaikuai et al., have explored the utility of using a new method based on subgroup tensor template-based groupwise registration to provide more accurate alignment of longitudinal infant brain tensor images. From a cohort of 27 typically developing infants, the authors studied three different registration approaches (i.e., the standard tensor-based registration, the standard FA-based registration, and their groupwise tensor-based registration) on 37 DTI scans for testing their registration accuracy. They also compared the impact of such methods on the registration accuracy when clustering images into subgroups. Particularly, they used four different metrics, such as Dyadic coherence, voxel-wise normalized standard FA deviations, normalized mutual information value, and the Jacobian determinant of the deformation generated during registration, to evaluate the performance of these registration approaches. Finally, they explored how the proposed intermediate subgroup tensor template-based groupwise registration performed across different clustering methods. Their findings suggest that both the standard tensor-based and intermediate subgroup tensor template-based groupwise registrations achieved better registration accuracy compared to the FA-based approach at both the global and local level, by providing smaller deviations of FA values and more defined gyri and sulci boundaries, respectively. They also observed that clustering by image similarity or by chronological age yielded comparable registration performance when using the intermediate subgroup tensor template-based groupwise registration. Moreover, they showed that performing intermediate subgroup tensor template-based groupwise registration without clustering (treating all infant scans as one group) resulted in lower registration accuracy at both affine and diffeomorphic transformation stages compared to clustering by image similarity. Finally, they found that their proposed method obtained an increased registration accuracy when varying either brain masks or the number of iterations during the affine and diffeomorphic transformation steps. The goal of the study is well accepted in the field and the overall idea of the study is properly designed. The text is generally well written, and the addition of explanatory details facilitates the understanding of the study to a more generalized audience. However, the organization of some paragraphs (and sub-paragraphs) should be slightly improved; for example, the introduction could be written without dividing it in different paragraphs, but by blending some concepts in a unique “block”. It is also highly encouraged a major improvement of the figures (in which crucial information are completely missing); such effort has been nicely done for some of the figures in the supplementary material which contain more descriptive information than the main ones. Although the study is well developed, a few methodological questions and concepts need to be further explored: • The “Registration of diffusion tensor images”, “Groupwise registration using intermediate templates”, and “Groupwise registration of infant tensor brain images using intermediate subgroup templates” paragraphs should be integrated inside the “Introduction” parts, without separating it from the rest of the speech. As it is right now, it is confusing for the reader. • Figure 1 (both panel A and B) needs work. The authors should use an actual slice of a scan, instead of green squares, triangles, and circles, and somehow show different groups of such scans based on their characteristics. Also, what does the dashed circle represent? The first level? This should be specified. The sample-specific common space is poorly represented as well. I am sure the authors have actual images to better explain these concepts. In the caption, it is better to set in bold font the “Illustration of (A) standard registration and (B) the proposed intermediate subgroup tensor template-based groupwise registration framework” phrase that represents the figure’s title. • Although the aims of the goal are well defined, the hypothesis (hypotheses) is (are) not stated. Thus, it is recommended to also add the hypotheses to help the readers understanding the overall purpose of the study and what the authors expect from the conducted analysis. • The author used “DTI-TK Diffusion Tensor Imaging ToolKit” for the standard tensor-based registration. However, such software is only for Linux and Mac/OS and this could be a limitation for readers who do not have such operating systems but would like to replicate the methods. Did the author explored other software compatible for other operating systems to perform such analysis? If yes, were the results different? • Which method was used to generate the 6-gof rigid body intermediate tensor? This information should be included in the “Standard tensor-based registration (DTI-TK)” paragraph for easy reproducibility of the study. • It is unclear if the “Generation of the initial target tensor template” paragraph is part of the previous one [i.e., “Standard tensor-based registration (DTI-TK)”] or not. My understanding is that this paragraph is the explanation of how the initial target tensor template was generated. Which software was used to generate the initial target tensor template? • It is highly encouraged to create a figure summarizing the methodology of the study; in particular, one that provide a simple overview of the steps performed for each registration approach. • The “Groupwise registration of infant tensor brain images using intermediate subgroup templates” paragraph confuses the reader on the next steps performed in the analysis. The similarity index between images was computed using the FA and MD maps; how were the values extracted? How was the distance of these DTI-derived metrics between images computed? Were these indices used for the Louvain clustering approach? • How was the Louvain clustering approach computed? • The link for the standard routine registration did not work (https://dti175tk.sourceforge.net/pmwiki/pmwiki.php/Documentation.FirstRegistration/). Can the authors provide the correct one? • It would be great if the authors can provide a more detailed descriptions on the differences between the one- and multiple-level alignment processes. • What is the rational of performing two rounds of standard tensor-based registration on the scans for the “no clustering” analysis? • Can the authors explain how were the four metrics to evaluate registration performance computed? Were they extracted using the DTI-TK software? If not, the authors should specify this information in the text. • The quality of all main figures is poor. Can the author provide a better resolution? Also, it is recommended to avoid acronyms in the caption (or at least explain them first), allowing the reader to better interpret each figure. • Although the authors somehow provided details, it is still difficult to do not get lost when reading the different terminologies (e.g., intermediate subgroup common space, sample-specific common space, groupwise registration, standard registration) used in the text. If possible, can the authors provide more insights for these terms to avoid possible confusion? • The registration accuracy of all methods was performed on a total of 37 DTI scans. However, without considering other variants, this can improve when a higher number of scans are considered. Can the authors provide evidence that such results do not change when varying the number of scans in each method? • It is highly encouraged to add a “Statistical Analysis” paragraph, summarizing all the tests performed to achieve the goals of the study. As of right now, this information is missing. • The authors should at least mentioned future applications of their method in other fields. For example, several studies in the epilepsy field explored the role of functional connectivity to identify those regions whose resection leads to seizure freedom (see Goodale et al., 2020; Corona et al., 2023; Shah et al., 2019; Lagarde et al., 2018), but only few of them explored how structural connections can influence functional connectivity. Thus, it would be interesting to propose as future investigation whether such template can be extended to pediatric populations and be used to provide a more accurate brain maps, which can be essential for studying brain connectivity, identify abnormal regions, and ultimately developing better treatments for epilepsy. Reviewer #2: The study by Shultz and colleagues addresses an important challenge in infant brain image registration: combining Louvain clustering with intermediate subgroup tensor templates, Shulz and collaborators approach offers a new solution tailored to the complexities of longitudinal infant brain image registration. This integration addresses the rapid developmental changes in infant brains, providing a more accurate and robust alignment method not previously reported in the literature. The method is logically and well presented as the clustering method and validation metrics. Crucially, the study compares multiple registration approaches (standard tensor-based, FA-based and intermediate subgroup registration), providing empirical support for the proposed method. The study introduces a novel framework for groupwise alignment of longitudinal infant DTI images by integrating Louvain clustering to create intermediate subgroup tensor templates, enhancing registration accuracy. Overall the manuscript is strong, but I have some considerations about it, I will completely support manuscript pubblication if they will be adressed: 1. which kind of correction for multiple comparisons is applied to the statistical comparisons? Author should better clarify this in the main text 2. Comparisons in the results are reported with p-values, but effect sizes are missing. Including effect sizes (Cohen’s d or standardized mean difference) would help quantify the significance of improvements. Since the p-values only indicate whether a difference is statistically significant. This will further clarify the strength of the effect beyond just statistical significance. 3. Instead of just reporting p-values, it would be better to provide 95% confidence intervals (CIs) for key statistics. CIs will help to interpret the precision of the effect size and whether the difference is practically meaningful. 4. The Discussion could better highlight the practical impact of this method in broader neuroimaging applications, beyond just registration accuracy improvements. 5. A more detailed discussion of limitations would strengthen the manuscript. Are there scenarios where this clustering method might not work well? Are there risks of overfitting to small datasets? ********** 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 ********** [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 |
| Revision 1 |
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Groupwise registration of infant brain diffusion tensor images using intermediate subgroup templates PONE-D-25-02132R1 Dear Dr. Shultz, 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, Federico Giove, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-25-02132R1 PLOS ONE Dear Dr. Shultz, 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 You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days 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. Federico Giove Academic Editor PLOS ONE |
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