Lumbar spine MRI annotation with intervertebral disc height and Pfirrmann grade predictions

Friska Natalia; Sud Sudirman; Daniel Ruslim; Ala Al-Kafri

doi:10.1371/journal.pone.0302067

Peer Review History

Original SubmissionFebruary 9, 2024
24 Mar 2024 Decision Letter - Koji Akeda, Editor PONE-D-24-05241Lumbar spine MRI annotation with intervertebral disc height and Pfirrmann grade predictionsPLOS ONE Dear Dr. Sudirman, 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 08 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. 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The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: “This work is supported, in part, by the Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia under grant number: 004-RD-LPPM-UMN/ P-HD/VI/2022.” We note that you have provided funding information that is currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “Initials of the authors who received each award: FN Grant numbers awarded to FN: 004-RD-LPPM-UMN/ P-HD/VI/2022. The full name of funder: the Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia URL of funder website: https://www.kemdikbud.go.id/ Did the sponsor or funder play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript? No” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 3. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. 4. 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: The manuscript is well written and basically acceptable after minor revision. Comments: 1. The manuscript should contain an Introduction, Materials and Methods, Results, Discussion, and Conclusion section. Please revise the manuscript. 2. The literature review section should be combined with the introduction section. These two sections are too long. Please summarize the content and shorten the descriptions. 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 ******** 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 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 ****** 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 ****** 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: We believe this study is useful in the context of the need to rationalize the need for new approaches to increase the efficiency and effectiveness of the radiological diagnostic process. I would like you to continue your research for more accuracy. Reviewer #2: The authors reported a fascinating application of deep learning in lumbar MRI analysis. By training a deep learning model on a large dataset of annotated MRI images with corresponding Pfirrmann grades, they developed a system that can automatically evaluate and grade intervertebral discs based on their appearance in the images. As the author pointed out in the discussion section, misclassification of 23.8% of IVDs that have Pfirrmann Grade 5 was a concern of this study (Misclassification of 30% of Pfirrmann Grade 1 IVDs as having Pfirrmann Grade 2 was not a problem because IVDs with both of Pfirrmann Grade 1 and 2 are healthy). Calculating the intervertebral disc height at three points (posterior, anterior, and midline) like "disc height index" might indeed provide a more comprehensive evaluation of disc morphology and potentially enhance the accuracy of the disc height assessment. I hope that this system will make steady progress and potentially assist radiologists in their diagnosis and treatment planning processes, as well as enable faster and more consistent evaluations across different healthcare settings. ****** 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 ******** 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. https://doi.org/10.1371/journal.pone.0302067.r001
Revision 1
26 Mar 2024 Author Response When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Our response: We have reviewed the manuscript again and have made the following changes based on the templates. • Moved the title down a few lines, remove the bold font style, and reduce the font size to 14. • We have also changed the way the headings are written to ensure that only the first word is capitalized. 2. Thank you for stating the following in the Acknowledgments Section of your manuscript: “This work is supported, in part, by the Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia under grant number: 004-RD-LPPM-UMN/ P-HD/VI/2022.” We note that you have provided funding information that is currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: “Initials of the authors who received each award: FN Grant numbers awarded to FN: 004-RD-LPPM-UMN/ P-HD/VI/2022. The full name of funder: the Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia URL of funder website: https://www.kemdikbud.go.id/ Did the sponsor or funder play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript? No” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Our response: We have removed the Acknowledgement section from the manuscript. The Funding Statement in the online submission form will remain the same. 3. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. Our response: In the last round of the peer-review process, we have already provided a publicly-shared folder on OneDrive where the reviewers can investigate the data that we used. The URL was https://bit.ly/PLOSPFG2024 We have now moved the data to Mendeley Data and can be accessed freely via the following URL: https://data.mendeley.com/datasets/x6ggzp2ycn/1 4. 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. Our response: We have checked the references to ensure that they are correctly cited and none of them had been retracted. We made the following changes: • Corrected reference [1] and [26] items which were incorrectly referred to as [Internet] because the reference manager has a URL in their record. • Updated the URL of reference [4] because the old one has changed. • Updated the last accessed date of all web page reference items [3, 4, 10, 17] to 25 March 2024 • Replaced reference item [30] with a new one due to the article’s recent retraction. The previous one was: 30. Chugh H, Gupta S, Garg M, Gupta D, Juneja S, Turabieh H, Na Y, Kiros Bitsue Z, Others. Image retrieval using different distance methods and color difference histogram descriptor for human healthcare. J Healthc Eng. 2022;2022. The new one is: 30. Hee-Hyung BuNam-Chul Kim Byoung-Ju Yun, Kim S-H. Content-Based Image Retrieval Using Multi-Resolution Multi-Direction Filtering-Based CLBP Texture Features and Color Autocorrelogram Features. J Inf Process Syst. 2020;16(4):991–1000. This change does not change or invalidate the statement in the manuscript in which the article was referenced. It was used to back up the argument that states “The majority of information in a color correlogram is concentrated along the main diagonal cells of the matrix hence several studies have suggested not to use the entire matrix but only these cells [30,31]”. The replacement article also supports the same argument. Additional Editor Comments: The manuscript is well written and basically acceptable after minor revision. Comments: 1. The manuscript should contain an Introduction, Materials and Methods, Results, Discussion, and Conclusion section. Please revise the manuscript. 2. The literature review section should be combined with the introduction section. These two sections are too long. Please summarize the content and shorten the descriptions. Our response: Thank you for the comments. We have reviewed the structure of our manuscript and made the following changes: • Combined the Introduction section and the Literature Review section into one section, and shorten the result by ~20%. • Replaced the title of the Methodology section to Materials and Methods, and • Replaced the title of the Experimental results and analysis section to Results and discussion. 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 ________________________________________ 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 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 ________________________________________ 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 ________________________________________ 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: We believe this study is useful in the context of the need to rationalize the need for new approaches to increase the efficiency and effectiveness of the radiological diagnostic process. I would like you to continue your research for more accuracy. Reviewer #2: The authors reported a fascinating application of deep learning in lumbar MRI analysis. By training a deep learning model on a large dataset of annotated MRI images with corresponding Pfirrmann grades, they developed a system that can automatically evaluate and grade intervertebral discs based on their appearance in the images. As the author pointed out in the discussion section, misclassification of 23.8% of IVDs that have Pfirrmann Grade 5 was a concern of this study (Misclassification of 30% of Pfirrmann Grade 1 IVDs as having Pfirrmann Grade 2 was not a problem because IVDs with both of Pfirrmann Grade 1 and 2 are healthy). Calculating the intervertebral disc height at three points (posterior, anterior, and midline) like "disc height index" might indeed provide a more comprehensive evaluation of disc morphology and potentially enhance the accuracy of the disc height assessment. I hope that this system will make steady progress and potentially assist radiologists in their diagnosis and treatment planning processes, as well as enable faster and more consistent evaluations across different healthcare settings. Our response: Thank you for your time and effort to review our paper. We are glad that both of you found our work to be useful and fascinating. The team hopes that we can build on this work and implement the solution more widely and increase its positive impact to society. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0302067.r002
27 Mar 2024 Decision Letter - Koji Akeda, Editor Lumbar spine MRI annotation with intervertebral disc height and Pfirrmann grade predictions PONE-D-24-05241R1 Dear Dr. Sudirman, 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, Koji Akeda Academic Editor PLOS ONE Additional Editor Comments (optional): This paper is a significant contribution and potentially be suitable for publication in PlosOne. Reviewers' comments: https://doi.org/10.1371/journal.pone.0302067.r003
Formally Accepted
29 Apr 2024 Acceptance Letter - Koji Akeda, Editor PONE-D-24-05241R1 PLOS ONE Dear Dr. Sudirman, 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. Koji Akeda Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0302067.r004

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