SummerSim 2017: Towards an Anatomical Modeling Pipeline for Neurosurgical Simulation and Shift-Corrected Navigation - Reviewer Jacob Barhak
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Jacob Barhak
May 27, 2017, 12:36:35 PM5/27/17
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Since this is public review, it is important to note that I know the main author and I solicited this work from him when I met him at the MSM/IMAG meeting at the NIH. This paper was reported as accepted to SpringSim, yet I was reported that it due to technicality never presented there. For this reason, I decided to ask the MSM SpringSim track chair for their review of this paper which was provided.
First the authors are requested to address the issues raised by the reviewer – Johannes Sametinger – which was the SpringSim MSM track co-chair. My understanding from verbal communications with the reviewer is that the review was enhanced beyond the SpringSim review– so the authors should read it carefully.
There was another reviewer that promised to provide review yet has not done it yet– if that reviewer delivers review, authors will be requested to address it. Until then, the authors should satisfy the 2 reviews that were delivered. Below is my response.
I read the paper and must add that it is very condensed. Much work has been invested by the authors in this direction and the authors are trying to give as complete view as possible to many activities going in their lab. In this paper the authors are combining multiple techniques together to allow then to eventually support neurosurgery. The techniques use atlas and deformable shapes that perform segmentation and triangulation.
The authors have published much work in the past and I myself witnessed a talk about an Atlas in SpringSim a few years ago. I also saw deformable shapes in the MSM/IMAG poster this year. So my question is what is the new angle in this paper that is much different than previous publications? If the authors emphasize this in the introduction or discussion, it will help focus on what is new. I know enough CAD to see that the authors did a lot of work, so I am inclined to accept the paper if the authors can show the new work and isolate it from previous work. If they can form a table/diagram of components, it may be even better than text – and if there is open source software available and they can put a link in the table – even better – yet I let the authors decide how they wish to present their work – the latter is just a suggestion.
Also if the authors have links to videos that show some of the images in movement – I would ask them to be added as links to this paper. Deformable shapes are best described via video.
Finally, please go over the paper once more and make sure details are correct – I have not checked equations, yet I saw that word marks some words as language issues and I did notice a double period at some point- this indicates that the paper needs another read and polish. If the authors fix this and satisfy another reviewer the paper should be accepted – yet a revision is needed.
It would also be nice if the authors add links to their review in the acknowledgment section – it will show complete record or the publication process.
Jacob Barhak
Jun 5, 2017, 1:24:49 PM6/5/17
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There was some correspondence regarding deadline reminders and the review process technicalities between the author and me that is omitted here. I am focusing on review after changes.
The paper has improved by answering some issues raised by the other reviewer.
However, the authors did not clarify what is new or try to assemble the bigger picture in a diagram like I asked. Nevertheless, those were just suggestions, so the paper is acceptable once the other reviewer concurs.
So the authors should make another version of the paper that corresponds to the template in the author kit. Otherwise, the paper will be blocked by the publication folk due to format. I noticed the references at the end and the last figure that seem out of format, yet there may be other issues. Please read the authors kit carefully. And since time is short and the absolute deadline is this week, please provide a diff between the original version and the new version to help reviewers decide fast.
I would ask again that while making the new version the authors will include links to the public reviews to make the publication record as complete as possible. This is a request, yet highly desirable considering the nature of review. Other paper in the BMPM track adopted this request.
If the other reviewer approves of the changes, the revised paper can be accepted for publication. Note that there seem to be no major issues with content of the paper and both reviewers are generally positive, it just need some work to fit the format. And this takes time which is short since the hard deadline is nearing.
Jacob Barhak
Jun 10, 2017, 8:01:07 PM6/10/17
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Since this review process was unusual it was decided to upload the entire communication between the author and reviewers. Some personal information was edited out and replaced with proper marks.
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Hi Michel,
One reviewer already provided a review for your paper. You will find it public in:
https://groups.google.com/forum/#!topic/public-scientific-reviews/KQOYxVLooBk
This is not final, since I located another reviewer that promised review. So you can expect another review within a couple of weeks. However, I thought that you would like to get quick notification to allow you time to react.
Jacob
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Thanks, Jacob. Keep me posted.
Cheers, Michel
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Hi Michel,
You may get your review last minute - I am still waiting for another reviewer to provide review - if I do not get it by tomorrow, you will get only two reviews - we typically try to provide 3 - 2 from external reviewers and one editorial. So you will get something by tomorrow.
For now, to keep things on a proper time table, please start making revisions - we have a tight time schedule and should notify authors by next week.
Hopefully this notification will help you speed things up on your side.
Jacob
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Hi Jacob,
I won't have time to make reviews until sometime next week. I have some grading to do for a summer class as well as a journal paper for which I have a tight deadline. I also have an entrepreneurship workshop at Babson College all of next week.
Cheers,
Michel
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So Michel,
You are not asked to do any reviews. I am just notifying you that your paper that you submitted to SummerSim has one reviewer who is delayed and since time schedule is tight, we will probably need to provide you one less review than we usually do.
We try to get you expert feedback whenever we can - in this case schedule is so tight that we may need to be satisfied with only two reviews which actually make this more difficult.
My request from you is that you take care of the revisions quickly once reviews arrive - You already have one review and I will provide another tomorrow.
If you have a time crunch, please feel free to delegate the work to the other co-authors.
Hopefully things are clear now.
Jacob
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Hi Michel,
As promised, you will find a second review public. You can find both reviews in these links:
https://groups.google.com/forum/#!topic/public-scientific-reviews/KQOYxVLooBk
https://groups.google.com/forum/#!topic/public-scientific-reviews/IxlT5LUpU-w
If you can satisfy both reviews the paper seems acceptable. If the other reviewer provides review, I will pass it to you for further comments - yet for now, please consider only those reviews.
And as for technicalities. Organizers need to notify authors within a couple of days - However, if you need a few more days for this paper, I will speak with organizers to extend this - after all we all want the best quality work.
Jacob
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Hi Jacob,
I will get through this Sunday or Monday.
Best wishes,
Michel
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Hi Michel,
You must have forgotten this. I assume you are very busy.
However, there is a hard deadline for this paper to get published. The camera ready deadline is nearing fast - June 12th and we need time to pass your response through the reviewers to get an ok before that, so the sooner you act the better.
Hopefully you can respond to the review today.
Jacob
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Hi Jacob,
I have not forgotten, but I've been at workshop that gobbles a lot of time and I also had time-consuming tasks by June 1st to activate a grant. I can get to it tonight.
Best wishes,
Michel
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Hi Michel,
This is a reminder.
There is a hard deadline for organizers as well and your paper needs revisions.
Please address this as soon as possible.
Jacob
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Hi Jacob,
I uploaded my paper Thursday evening. Did you not see it? Please advise.
Best wishes
Michel
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Hi again,
this is what I uploaded. Is there are copyright form I need to fill out?
Best wishes,
Michel
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Sorry Michel,
Indeed you have uploaded the paper, yet I figured you will notify me and add a few response words for the review. Typically that is the custom, so I was looking for an email from you - the system does not automatically notify me if changes.
I'll pass the new version for review.
Thanks for answering quickly.
Jacob
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So Michel,
Once the paper as accepted you get an automated notification with a link to a form in which you have to upload the camera ready version and the response for reviewers along side several forms.
We are not there yet - we are still reviewing. The next stage with this paper is for reviewers to check that your new version answers their review issues.
Many authors provide a detailed answer to the reviewers about changes made what was changed in the paper to save the reviewers time - it also create a discussion that can later accompany the paper.
Here are some examples by authors for this track:
https://groups.google.com/forum/#!topic/public-scientific-reviews/_W8IQj0TkRM
https://groups.google.com/forum/#!topic/public-scientific-reviews/TRVhCMbwzLI
https://groups.google.com/forum/#!topic/public-scientific-reviews/KHREQiTyErc
If you can send me those by email it will speed up matters. Otherwise reviewers need to read the entire paper again to find the changes. This response is also later uploaded to the system upon final notification.
Also if you have the last version and create a diff, it would save review time and help speed up matters - it just take a few minute for you to create it if you have both versions.
I should have mentioned this before. Apologies. Hopefully it is easy to accommodate.
Jacob
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Hi Jacob,
I have Acrobat Pro at my office. I can do a difference file with that by end of the day Monday, and respond with the details you want by then.
Best wishes,
Michel
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Hi Michel,
Below are links to your second review round:
https://groups.google.com/forum/#!topic/public-scientific-reviews/KQOYxVLooBk
https://groups.google.com/forum/#!topic/public-scientific-reviews/IxlT5LUpU-w
Look for the second post in each link for the new review.
Please provide a revised version that answers the reviewers. Please also prepare a reply for reviewers document - you will need it for final submission.
However, please do it as fast as possible. According to main organizers the hard deadline is June 12th - according to the contract with publishers. Reviewers need to approve your paper before that so you can get a link to upload the final submission with the copyright forms - otherwise it ends up in the WIP track without getting published although it can be presented. And reviewers need time to react to your post - we are human as well, so you should give us time and not submit at the last minute.
If you can shorten our review time by providing a diff version and some text about the changes you made, it would help speed up the process tremendously.
Hopefully it is possible on your side.
Jacob
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Okay, I will look at it this afternoon.
Michel
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Hi Jacob,
the problem with the interface is that it allows just one pdf to be uploaded and seems to prefer the pdf format. Your website should reflect the review process!
I just uploaded the diff file, but that overwrote the final version that I uploaded. In any event, here is the "final" version I submitted last week, the version that was submitted originally, and the diff file.
I simply did not have enough time for a major rewrite, given my participation in the week-long workshop at Babson College and the urgent submission I needed to do of an IRB approval by June 1 to make my funding from Alzheimer's Association available, after which date the funding would have been withdrawn. Unfortunately, the SCS paper has suffered.
I do not have the Word version with me right now (on my laptop which I used last week while at Babson). I neglected to update the footer last time. I will send you the Word file tonight with the updated footer for SummerSim; I can upload that version online if you want. My apologies for that oversight. Once again, I will tweak the footer tonight.
Best wishes,
Michel
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Ok Michel,
You are right that the web site does not reflect the review process. The BMPM track has the exploratory public review process that is not fully yet supported by a system. This forces chairs to do extra work and make sure records are kept in two systems for compliance - the Start system for SCS and the public portal through Google groups. In many cases we rely on email to pass information. In some cases we publish entire email conversations. If you have no objection, I want to publish this entire conversation thread so others will know what process we go through before publication - it will help both student and publishers in the future. Apologies for the inconvenience, yet we are trying to make publication as transparent as possible within limitations - some technical - some human. And this is a last minute submission so we are pressed even further.
Specifically for your paper - I am attaching your previous word version - It was left on my machine after my first review. Hopefully it will help you make comparisons in the future.
I will pass the diff version to Johannes in hope it is enough for him to make a decision. Yet you will have to comply with the authors kit in the final version - so there is still work to do. Even if we accept this version, the publication chair may return it for editing to comply with format - this happened in the past.
Many thanks for the quick replies - it helps speed up things.
Jacob
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Hi again,
as I mentioned in my previous email, I will upload the final version based on the Word file that I do not have here. My problem was that on my laptop I had only a Word version of the second-last file submitted in the past SCS17_Audette11317c.docx, but only a pdf version of the submitted file SCS17_Audette11317d.pdf. I tried to update the 17c.doc file to reflect the updates of 17d, prior to making the review updates, however I left out the footer for SummerSim (one of the edits found in 17d but not 17c), which fell through the cracks this time. The other edits of 17d were incorporated into 17c, prior to doing Johannes' recommended edits, the final version of which was SCS17_Audette11317Final. Foolishly, I neglected to update the edit date.
I will make the changes to the Word file tonight to the footer, and (for the same low price) update the final edit date.
My apologies for that oversight. Bear with me.
Cheers,
Michel
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Thanks Michel,
Johannes and I will wait for an email from you with the revised version with a diff from original file I just sent you. After that we can make a decision.
Unless you have reservations, I will make this email conversation public as part of the public review once we are done. Let me know if you object or what to omit something - we are using informal language here - yet I really would like to show folk what the publication process is all about and things that happen in it.
Again, the paper is not in bad shape - its just time consuming formatting that seems to be the issue.
Jacob
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Gents,
here is the final paper with the footnote corrected, in Word format. No changes were made to the text otherwise, except for some reformatting as I found some dead space that I wanted to take out. The diff file that I sent earlier today still applies from a content perspective.
Also, if accepted, can you let me know what part of the conference coincides with the biomedical track?
Keep me posted and thanks for your continued support.
Michel
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So Michel,
You will need another version - so better do it early.
Please check the author kit again for this year.
They changed the format of the references from previous years - I myself was surprised by the new format. Robert pointed out the changes to me. Look where they put the commas. Also look on how they ask for tables and figures to appear - they do not show figures surrounded by text like your last figure.
Look, the content seems to be ok - both reviewers are generally positive - its the formatting that needs fixing.
If the paper gets accepted as is, there is a good chance that the publication chair will return it to you for changes. At this point there will be even less time for you to respond and the paper may fall on a technicality - do you really want this to happen?
I am unsure about details with agreed with the publishers - yet if you follow the authors kit - there should be no problems.
Also, please read again my comment about adding links to the reviewers - your current version ignored this request and this is not the first time I am asking. If you omit reference to the reviewers, then you may be in the minority since other papers did include such reference. You see, we are trying to transform the review process to give value to the reviewers - please support us there if you believe reviewers should get credit for their effort - it really means just adding two lines in the acknowledgment with two hyperlinks.
Hopefully your next version will fix this.
Jacob
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Okay, I will reformat it tonight.
Michel
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Gents,
I'm about to upload this file. I saved the citations as static and manually tweaked them to meet the template format (Word does not seem to do all of these natively). I also reformatted the last figure and acknowledged the reviewers.
Best wishes,
Michel
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Woops. Small typo at the end, now removed.
Michel Audette, Ph.D.
Associate Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
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Thanks Michel,
This version seems fine to me.
If Johannes approves we can proceed to the final upload.
Johannes, are you ok with this version?
Hopefully Johannes can respond fast.
Jacob
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Hi again,
Can you tell me the precise date for the biomedical track? I may not stay for the whole conference.
*** some personal information was deleted and explains why the author date constraints ***
Cheers,
Michel
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So Michel,
Since you are sending personal information, I will omit this from the review record.
The schedule can be decided only after organizers know how many papers are in.
However, there were several requests to make the track early in the conference, so I will ask organizers to place the track on July 10th. This seems to be a common date that should be good for all presenters.
However, we will know schedule only next week after all final versions of papers are in.
I think we should be able to accommodate all presenter preferences.
Jacob
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Hi Jacob,
Sorry for the belated reply. I had a look at the two versions and at my previous comments. I have added remarks on these below. My previous comments are shown in red.
Best Johannes
The title says "... and shift-corrected navigation". I can neither find anything about shift-correction nore about navigation in the paper. Navigation is mentioned in the first sentence of each the abstract and the introduction, and neuronavigation is briefly mentioned in Section 3. But that's it.
I also can't find the word pipeline in the paper other than in the title.
I cannot see anything that addresses this issue.
Section 2 is quite extensive. It is rather hard for the reader to distinguish between fundamentals and ongoing work, especially in the authors' group. Section 2.1 is entitled Background, but it starts with "Our group emphasizes ...". Are all subsections desrbibing your actual work? An overview of the paper at the end of Section 1 may also help. Is Section 2 supposed to describe the pipline you mention in the title? Is Section 3 the core of your paper? If yes, it's rather short.
Again, I cannot see anything that addresses this issue.
In the conclusion, the authors say that they were describing ongoing work. So what is the contribution of this paper? To get an idea of what the authors are doing? This can be okay, but I'd expect a better presentation of general background and challenges, and what the authors are suggesting to address these challenges.
Same as above.
The ‘minor things’ shown below apparently have been corrected.
page 1: MRI and CT are probably known by all readers. Yet, I would define these acronyms.
page 2: header: two authors are missing
page 2: figure -> Figure (everywhere)
page 3: incomplete reference (CGAL,)
page 3: categories of tetrahedralization: what about optimization-based?
Figure 2: What does WPI stand for?
page 4: avoid italics and underline
Fig. 5: text is distorted. Do you need Fig. 5? Only some of it is mentioned in the text very shortly.
all figures: colors won't be visible in black/white printing, references to colors will confuse readers
all figures: I suggest to use short titles and to move explanations to the text.
all citations: mention year: (Delingette H) -> (Delingette 1999), see author guidelines
Incomplete references, e.g.:
- ContourWorks requires authentication
- (Haq R 15b) is incomplete.
- (Haq R 15c) accepted? in 2015?
- Doulbe period in (Lorensen 1987)
- What does n.d. stand for in (FreeSurfer), (Protege)?
- ,: and ,, in (Ju 2002)
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Hi Johannes,
I can emphasize the shift-corrected navigation in the presentation, or I don't mind adding a few sentences in the paper if there is time. I missed it completely. The shared-surface deep brain model is being developed to compensate brain shift in deep brain stimulation, towards a robotic DBS assistant underway at Worcester Polytechnic.
Let me know if there is still time to tweak the paper, gents.
Michel
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So Michel,
There is still time to make changes in the paper, yet we should really finish within a day or two. After that it becomes too close to the absolute deadline - we are already on borrowed time.
You convinced me. If Johannes is ok with your answers, we can proceed to final upload. Until then please use email to communicate to speed up matters and and CC me and Robert to the conversation so we can make it public at the end.
I thank Johannes for his quick responses that help us advance.
Jacob
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Jacob, I suggest it’s up to you now. You know what my concerns were and you can see how they were and will be addressed. If Michel provides a new version, you can look at the three points that I had raised, I think you will be able to make a quick decision. Best Johannes
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Thanks Johanness,
So Michel, if you can add a few sentences in the paper to answer the three unanswered issues Johanness raised, we should be good. If you can point out where you add them in the next version, it will save me time.
The sooner, the better.
Jacob
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Gents,
Here is an updated version. I have tweaked the title and added an author as well. I may ask this student, Lucas Potter, to do the presentation in my stead (he is involved in the spine work and is the best speaker of my current PhD students). I'm having a bit of a tough negotiation with my wife about my participation, given that I had a number of trips in May.
I have made the explanation on brain shift more explicit. The main section is section 2, and the longer title makes the contribution more apparent.
Tomorrow I may not be able to access my mail,
*** some personal details about availability were deleted as those are not relevant for review ***
I will check my email this weekend to see if something is needed.
Best wishes,
Michel
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Ok Michel,
You made some changes to the title and added a few paragraphs about DBS.
I went back to check if you answered the 3 issues Johannes raised:
1. Title not representative of content - Your change of title and the added paragraph that explain why shift correction is important are a good fix.
2. Section 2 is short and not focused - You did extend the section and it is now a bit clearer why you need those computational techniques. However, I still think that there is too much information in the paper without some map or diagram that shows where all the methods you develop help - and there are quite a few techniques you use. Nevertheless, I do not think this should block publication - if a reader does not understand how those techniques come together they can always contact the authors - so although the solution is not perfect, it is acceptable in my opinion.
3. Background, challenges and innovation. Your paragraph does give more background and explain importance. The changes of title brings better focus to what is new and you help the reader. I think it is ok, although I really would have liked to see some diagram or table showing all the techniques you use. Yet again, this is only wishful thinking on my side and I think your solution is sufficient.
So I think you addressed all of the issues Johannes raised. Johannes is CCd and can correct me if I am wrong. So from this perspective I think the paper is acceptable.
However, I do have issues with adding an author at this point. This practice of adding authors to a paper during review is unusual and undesirable and can be abused considering current academic practices. Yet I have seen this happen a few times by now and it always causes delays and extra effort. When I see this issue and I react the same way, I stop the process and ask the new author to explain their contribution to the paper and the corresponding author to explain why the author did not appear in the initial submission. It is important to keep this record for the publisher.
So please Michel, please forward this email to the new author as soon as possible so he can explain his contribution and provide an explanation on why was that author not in the initial list of authors.
Once those explanations are provided and satisfactory, and as long as Robert or Johannes do not object to my decision, the paper can be accepted in the version you sent.
Please note that this review becomes public in this track - so please no more personal details about family unless you want to share those with the public. I intend to omit personal details from the review record.
As for presentation, as long as someone can properly present your work even if you cannot arrive, it would be fine - although we would prefer the best expert possible.
Hopefully we can finish the review process quickly to allow you to upload all the forms to the system.
Jacob
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Hi Jacob,
my response is copied to Lucas, who will contact you with his contribution.
Best wishes,
Michel
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Hi Lucas,
Since you were added as an author late during the review process, we need to look at details.
Can you please describe your contribution to the paper?
And if your contribution is substantial Michel should explain why you were not included beforehand.
Please do this as soon as possible since time is running out - hopefully you can do this today.
Jacob
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Dr. Barham,
I apologize for my delayed response. I was not part of the original team writing the paper, but I am working on the application of dual contouring technique to scoliosis surgery (see the last paragraph of section 2.3).
Regards,
Lucas Potter
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Thanks Lucas,
This complicates things. It is a paper that adds many elements together. So your work was probably referenced to some degree. Yet your name does not appear in the references quoted in the work like [Rashid] , so I assume your work is relatively new, perhaps corresponding to the last line in the paragraph. Please correct me if I am wrong.
I suspect that your name was added mostly due to presentation constraints. If this was the main reason for adding your name, then it was not necessary. The lab can still send you to present the work without being an author in the paper. The presenter does not have to be an author - although its highly desirable.
However, if you add new material to the paper that describes your recent findings that support the paper, then you can be added as an author. However, this must be done within a day since we are pressing against a deadline that is hard and all the proper documents and forms must be uploaded before June 12 - which also takes time. The other option is removing your name.
So in summary there are two choices to get the paper accepted:
1. Remove your name from the author list.
2. Keep your name and add sufficient material to justify adding your name as an author.
Whatever path you choose should be done quickly with a final version submitted tomorrow.
Hopefully this time table is possible.
Jacob
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Hi Jacob,
Okay, if it's easier then, I will remove Lucas' name as an author and still direct him to make the presentation. Lucas' contribution coincides more with the future of the project than what has been achieved so far.
Lucas, I will contact you with an expense account with which to plan your travel; I will ask MSVE admin assistant Jayne Massey to help you. Please get familiar with the paper. I will dig up some similar slides as well as ask the other students to also provide you with some. You can easily dig up images from the doc file itself.
My apologies for the false start.
Michel Audette, Ph.D.
Associate Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
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Ok Michel,
This version is acceptable.
You can proceed to final upload. Look at your email - you should have received an automated email of acceptance with a link to the final submission form.
You will need 4 documents:
1. The final pdf manuscript
2.The original that created the pdf - in your case it is the doc format document
3. The copyright firm filled - there are two pages there - make sure you sign both. Here is the link to the form:
http://scs.org/wp-content/uploads/2016/10/AuthorsKitForms-TransferOfCopyrightAuthorCert.pdf
4. A response for reviewers. You can just copy and paste our email conversation that I will make available in the following link in about half an hour:
https://groups.google.com/forum/#!topic/public-scientific-reviews/IxlT5LUpU-w
I do still allow the option of keeping Lucas's name in the last version you upload if some of his latest work is reported as well - beyond what is in the paper now. However, I suggest that you first upload the version you sent me since the hard deadline I was given is June 12th and the authors do not wish to fall on a technicality.
Once you upload, if you want to work more and add a few words about Lucas's newer work to allow him as an author, send me a new version by email and if It is substantial enough and there still time, it may be possible. However, it is awfully close to the deadline and it may be better to leave this for future publication.
Sorry for the less than immediate response, I just saw your message now - for some reason it was not marked as new by my mailer. Hopefully you get it in time.
Jacob
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Hi Michel,
One reviewer already provided a review for your paper. You will find it public in:
https://groups.google.com/forum/#!topic/public-scientific-reviews/KQOYxVLooBk
This is not final, since I located another reviewer that promised review. So you can expect another review within a couple of weeks. However, I thought that you would like to get quick notification to allow you time to react.
Jacob
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Thanks, Jacob. Keep me posted.
Cheers, Michel
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Hi Michel,
You may get your review last minute - I am still waiting for another reviewer to provide review - if I do not get it by tomorrow, you will get only two reviews - we typically try to provide 3 - 2 from external reviewers and one editorial. So you will get something by tomorrow.
For now, to keep things on a proper time table, please start making revisions - we have a tight time schedule and should notify authors by next week.
Hopefully this notification will help you speed things up on your side.
Jacob
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Hi Jacob,
I won't have time to make reviews until sometime next week. I have some grading to do for a summer class as well as a journal paper for which I have a tight deadline. I also have an entrepreneurship workshop at Babson College all of next week.
Cheers,
Michel
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So Michel,
You are not asked to do any reviews. I am just notifying you that your paper that you submitted to SummerSim has one reviewer who is delayed and since time schedule is tight, we will probably need to provide you one less review than we usually do.
We try to get you expert feedback whenever we can - in this case schedule is so tight that we may need to be satisfied with only two reviews which actually make this more difficult.
My request from you is that you take care of the revisions quickly once reviews arrive - You already have one review and I will provide another tomorrow.
If you have a time crunch, please feel free to delegate the work to the other co-authors.
Hopefully things are clear now.
Jacob
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Hi Michel,
As promised, you will find a second review public. You can find both reviews in these links:
https://groups.google.com/forum/#!topic/public-scientific-reviews/KQOYxVLooBk
https://groups.google.com/forum/#!topic/public-scientific-reviews/IxlT5LUpU-w
If you can satisfy both reviews the paper seems acceptable. If the other reviewer provides review, I will pass it to you for further comments - yet for now, please consider only those reviews.
And as for technicalities. Organizers need to notify authors within a couple of days - However, if you need a few more days for this paper, I will speak with organizers to extend this - after all we all want the best quality work.
Jacob
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Hi Jacob,
I will get through this Sunday or Monday.
Best wishes,
Michel
############
Hi Michel,
You must have forgotten this. I assume you are very busy.
However, there is a hard deadline for this paper to get published. The camera ready deadline is nearing fast - June 12th and we need time to pass your response through the reviewers to get an ok before that, so the sooner you act the better.
Hopefully you can respond to the review today.
Jacob
############
Hi Jacob,
I have not forgotten, but I've been at workshop that gobbles a lot of time and I also had time-consuming tasks by June 1st to activate a grant. I can get to it tonight.
Best wishes,
Michel
############
Hi Michel,
This is a reminder.
There is a hard deadline for organizers as well and your paper needs revisions.
Please address this as soon as possible.
Jacob
############
Hi Jacob,
I uploaded my paper Thursday evening. Did you not see it? Please advise.
Best wishes
Michel
############
Hi again,
this is what I uploaded. Is there are copyright form I need to fill out?
Best wishes,
Michel
############
Sorry Michel,
Indeed you have uploaded the paper, yet I figured you will notify me and add a few response words for the review. Typically that is the custom, so I was looking for an email from you - the system does not automatically notify me if changes.
I'll pass the new version for review.
Thanks for answering quickly.
Jacob
############
So Michel,
Once the paper as accepted you get an automated notification with a link to a form in which you have to upload the camera ready version and the response for reviewers along side several forms.
We are not there yet - we are still reviewing. The next stage with this paper is for reviewers to check that your new version answers their review issues.
Many authors provide a detailed answer to the reviewers about changes made what was changed in the paper to save the reviewers time - it also create a discussion that can later accompany the paper.
Here are some examples by authors for this track:
https://groups.google.com/forum/#!topic/public-scientific-reviews/_W8IQj0TkRM
https://groups.google.com/forum/#!topic/public-scientific-reviews/TRVhCMbwzLI
https://groups.google.com/forum/#!topic/public-scientific-reviews/KHREQiTyErc
If you can send me those by email it will speed up matters. Otherwise reviewers need to read the entire paper again to find the changes. This response is also later uploaded to the system upon final notification.
Also if you have the last version and create a diff, it would save review time and help speed up matters - it just take a few minute for you to create it if you have both versions.
I should have mentioned this before. Apologies. Hopefully it is easy to accommodate.
Jacob
############
Hi Jacob,
I have Acrobat Pro at my office. I can do a difference file with that by end of the day Monday, and respond with the details you want by then.
Best wishes,
Michel
############
Hi Michel,
Below are links to your second review round:
https://groups.google.com/forum/#!topic/public-scientific-reviews/KQOYxVLooBk
https://groups.google.com/forum/#!topic/public-scientific-reviews/IxlT5LUpU-w
Look for the second post in each link for the new review.
Please provide a revised version that answers the reviewers. Please also prepare a reply for reviewers document - you will need it for final submission.
However, please do it as fast as possible. According to main organizers the hard deadline is June 12th - according to the contract with publishers. Reviewers need to approve your paper before that so you can get a link to upload the final submission with the copyright forms - otherwise it ends up in the WIP track without getting published although it can be presented. And reviewers need time to react to your post - we are human as well, so you should give us time and not submit at the last minute.
If you can shorten our review time by providing a diff version and some text about the changes you made, it would help speed up the process tremendously.
Hopefully it is possible on your side.
Jacob
############
Okay, I will look at it this afternoon.
Michel
############
Hi Jacob,
the problem with the interface is that it allows just one pdf to be uploaded and seems to prefer the pdf format. Your website should reflect the review process!
I just uploaded the diff file, but that overwrote the final version that I uploaded. In any event, here is the "final" version I submitted last week, the version that was submitted originally, and the diff file.
I simply did not have enough time for a major rewrite, given my participation in the week-long workshop at Babson College and the urgent submission I needed to do of an IRB approval by June 1 to make my funding from Alzheimer's Association available, after which date the funding would have been withdrawn. Unfortunately, the SCS paper has suffered.
I do not have the Word version with me right now (on my laptop which I used last week while at Babson). I neglected to update the footer last time. I will send you the Word file tonight with the updated footer for SummerSim; I can upload that version online if you want. My apologies for that oversight. Once again, I will tweak the footer tonight.
Best wishes,
Michel
############
Ok Michel,
You are right that the web site does not reflect the review process. The BMPM track has the exploratory public review process that is not fully yet supported by a system. This forces chairs to do extra work and make sure records are kept in two systems for compliance - the Start system for SCS and the public portal through Google groups. In many cases we rely on email to pass information. In some cases we publish entire email conversations. If you have no objection, I want to publish this entire conversation thread so others will know what process we go through before publication - it will help both student and publishers in the future. Apologies for the inconvenience, yet we are trying to make publication as transparent as possible within limitations - some technical - some human. And this is a last minute submission so we are pressed even further.
Specifically for your paper - I am attaching your previous word version - It was left on my machine after my first review. Hopefully it will help you make comparisons in the future.
I will pass the diff version to Johannes in hope it is enough for him to make a decision. Yet you will have to comply with the authors kit in the final version - so there is still work to do. Even if we accept this version, the publication chair may return it for editing to comply with format - this happened in the past.
Many thanks for the quick replies - it helps speed up things.
Jacob
############
Hi again,
as I mentioned in my previous email, I will upload the final version based on the Word file that I do not have here. My problem was that on my laptop I had only a Word version of the second-last file submitted in the past SCS17_Audette11317c.docx, but only a pdf version of the submitted file SCS17_Audette11317d.pdf. I tried to update the 17c.doc file to reflect the updates of 17d, prior to making the review updates, however I left out the footer for SummerSim (one of the edits found in 17d but not 17c), which fell through the cracks this time. The other edits of 17d were incorporated into 17c, prior to doing Johannes' recommended edits, the final version of which was SCS17_Audette11317Final. Foolishly, I neglected to update the edit date.
I will make the changes to the Word file tonight to the footer, and (for the same low price) update the final edit date.
My apologies for that oversight. Bear with me.
Cheers,
Michel
############
Thanks Michel,
Johannes and I will wait for an email from you with the revised version with a diff from original file I just sent you. After that we can make a decision.
Unless you have reservations, I will make this email conversation public as part of the public review once we are done. Let me know if you object or what to omit something - we are using informal language here - yet I really would like to show folk what the publication process is all about and things that happen in it.
Again, the paper is not in bad shape - its just time consuming formatting that seems to be the issue.
Jacob
############
Gents,
here is the final paper with the footnote corrected, in Word format. No changes were made to the text otherwise, except for some reformatting as I found some dead space that I wanted to take out. The diff file that I sent earlier today still applies from a content perspective.
Also, if accepted, can you let me know what part of the conference coincides with the biomedical track?
Keep me posted and thanks for your continued support.
Michel
############
So Michel,
You will need another version - so better do it early.
Please check the author kit again for this year.
They changed the format of the references from previous years - I myself was surprised by the new format. Robert pointed out the changes to me. Look where they put the commas. Also look on how they ask for tables and figures to appear - they do not show figures surrounded by text like your last figure.
Look, the content seems to be ok - both reviewers are generally positive - its the formatting that needs fixing.
If the paper gets accepted as is, there is a good chance that the publication chair will return it to you for changes. At this point there will be even less time for you to respond and the paper may fall on a technicality - do you really want this to happen?
I am unsure about details with agreed with the publishers - yet if you follow the authors kit - there should be no problems.
Also, please read again my comment about adding links to the reviewers - your current version ignored this request and this is not the first time I am asking. If you omit reference to the reviewers, then you may be in the minority since other papers did include such reference. You see, we are trying to transform the review process to give value to the reviewers - please support us there if you believe reviewers should get credit for their effort - it really means just adding two lines in the acknowledgment with two hyperlinks.
Hopefully your next version will fix this.
Jacob
############
Okay, I will reformat it tonight.
Michel
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Gents,
I'm about to upload this file. I saved the citations as static and manually tweaked them to meet the template format (Word does not seem to do all of these natively). I also reformatted the last figure and acknowledged the reviewers.
Best wishes,
Michel
############
Woops. Small typo at the end, now removed.
Michel Audette, Ph.D.
Associate Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
############
Thanks Michel,
This version seems fine to me.
If Johannes approves we can proceed to the final upload.
Johannes, are you ok with this version?
Hopefully Johannes can respond fast.
Jacob
############
Hi again,
Can you tell me the precise date for the biomedical track? I may not stay for the whole conference.
*** some personal information was deleted and explains why the author date constraints ***
Cheers,
Michel
############
So Michel,
Since you are sending personal information, I will omit this from the review record.
The schedule can be decided only after organizers know how many papers are in.
However, there were several requests to make the track early in the conference, so I will ask organizers to place the track on July 10th. This seems to be a common date that should be good for all presenters.
However, we will know schedule only next week after all final versions of papers are in.
I think we should be able to accommodate all presenter preferences.
Jacob
############
Hi Jacob,
Sorry for the belated reply. I had a look at the two versions and at my previous comments. I have added remarks on these below. My previous comments are shown in red.
Best Johannes
The title says "... and shift-corrected navigation". I can neither find anything about shift-correction nore about navigation in the paper. Navigation is mentioned in the first sentence of each the abstract and the introduction, and neuronavigation is briefly mentioned in Section 3. But that's it.
I also can't find the word pipeline in the paper other than in the title.
I cannot see anything that addresses this issue.
Section 2 is quite extensive. It is rather hard for the reader to distinguish between fundamentals and ongoing work, especially in the authors' group. Section 2.1 is entitled Background, but it starts with "Our group emphasizes ...". Are all subsections desrbibing your actual work? An overview of the paper at the end of Section 1 may also help. Is Section 2 supposed to describe the pipline you mention in the title? Is Section 3 the core of your paper? If yes, it's rather short.
Again, I cannot see anything that addresses this issue.
In the conclusion, the authors say that they were describing ongoing work. So what is the contribution of this paper? To get an idea of what the authors are doing? This can be okay, but I'd expect a better presentation of general background and challenges, and what the authors are suggesting to address these challenges.
Same as above.
The ‘minor things’ shown below apparently have been corrected.
page 1: MRI and CT are probably known by all readers. Yet, I would define these acronyms.
page 2: header: two authors are missing
page 2: figure -> Figure (everywhere)
page 3: incomplete reference (CGAL,)
page 3: categories of tetrahedralization: what about optimization-based?
Figure 2: What does WPI stand for?
page 4: avoid italics and underline
Fig. 5: text is distorted. Do you need Fig. 5? Only some of it is mentioned in the text very shortly.
all figures: colors won't be visible in black/white printing, references to colors will confuse readers
all figures: I suggest to use short titles and to move explanations to the text.
all citations: mention year: (Delingette H) -> (Delingette 1999), see author guidelines
Incomplete references, e.g.:
- ContourWorks requires authentication
- (Haq R 15b) is incomplete.
- (Haq R 15c) accepted? in 2015?
- Doulbe period in (Lorensen 1987)
- What does n.d. stand for in (FreeSurfer), (Protege)?
- ,: and ,, in (Ju 2002)
############
Hi Johannes,
I can emphasize the shift-corrected navigation in the presentation, or I don't mind adding a few sentences in the paper if there is time. I missed it completely. The shared-surface deep brain model is being developed to compensate brain shift in deep brain stimulation, towards a robotic DBS assistant underway at Worcester Polytechnic.
Let me know if there is still time to tweak the paper, gents.
Michel
############
So Michel,
There is still time to make changes in the paper, yet we should really finish within a day or two. After that it becomes too close to the absolute deadline - we are already on borrowed time.
You convinced me. If Johannes is ok with your answers, we can proceed to final upload. Until then please use email to communicate to speed up matters and and CC me and Robert to the conversation so we can make it public at the end.
I thank Johannes for his quick responses that help us advance.
Jacob
############
Jacob, I suggest it’s up to you now. You know what my concerns were and you can see how they were and will be addressed. If Michel provides a new version, you can look at the three points that I had raised, I think you will be able to make a quick decision. Best Johannes
############
Thanks Johanness,
So Michel, if you can add a few sentences in the paper to answer the three unanswered issues Johanness raised, we should be good. If you can point out where you add them in the next version, it will save me time.
The sooner, the better.
Jacob
############
Gents,
Here is an updated version. I have tweaked the title and added an author as well. I may ask this student, Lucas Potter, to do the presentation in my stead (he is involved in the spine work and is the best speaker of my current PhD students). I'm having a bit of a tough negotiation with my wife about my participation, given that I had a number of trips in May.
I have made the explanation on brain shift more explicit. The main section is section 2, and the longer title makes the contribution more apparent.
Tomorrow I may not be able to access my mail,
*** some personal details about availability were deleted as those are not relevant for review ***
I will check my email this weekend to see if something is needed.
Best wishes,
Michel
############
Ok Michel,
You made some changes to the title and added a few paragraphs about DBS.
I went back to check if you answered the 3 issues Johannes raised:
1. Title not representative of content - Your change of title and the added paragraph that explain why shift correction is important are a good fix.
2. Section 2 is short and not focused - You did extend the section and it is now a bit clearer why you need those computational techniques. However, I still think that there is too much information in the paper without some map or diagram that shows where all the methods you develop help - and there are quite a few techniques you use. Nevertheless, I do not think this should block publication - if a reader does not understand how those techniques come together they can always contact the authors - so although the solution is not perfect, it is acceptable in my opinion.
3. Background, challenges and innovation. Your paragraph does give more background and explain importance. The changes of title brings better focus to what is new and you help the reader. I think it is ok, although I really would have liked to see some diagram or table showing all the techniques you use. Yet again, this is only wishful thinking on my side and I think your solution is sufficient.
So I think you addressed all of the issues Johannes raised. Johannes is CCd and can correct me if I am wrong. So from this perspective I think the paper is acceptable.
However, I do have issues with adding an author at this point. This practice of adding authors to a paper during review is unusual and undesirable and can be abused considering current academic practices. Yet I have seen this happen a few times by now and it always causes delays and extra effort. When I see this issue and I react the same way, I stop the process and ask the new author to explain their contribution to the paper and the corresponding author to explain why the author did not appear in the initial submission. It is important to keep this record for the publisher.
So please Michel, please forward this email to the new author as soon as possible so he can explain his contribution and provide an explanation on why was that author not in the initial list of authors.
Once those explanations are provided and satisfactory, and as long as Robert or Johannes do not object to my decision, the paper can be accepted in the version you sent.
Please note that this review becomes public in this track - so please no more personal details about family unless you want to share those with the public. I intend to omit personal details from the review record.
As for presentation, as long as someone can properly present your work even if you cannot arrive, it would be fine - although we would prefer the best expert possible.
Hopefully we can finish the review process quickly to allow you to upload all the forms to the system.
Jacob
############
Hi Jacob,
my response is copied to Lucas, who will contact you with his contribution.
Best wishes,
Michel
############
Hi Lucas,
Since you were added as an author late during the review process, we need to look at details.
Can you please describe your contribution to the paper?
And if your contribution is substantial Michel should explain why you were not included beforehand.
Please do this as soon as possible since time is running out - hopefully you can do this today.
Jacob
############
Dr. Barham,
I apologize for my delayed response. I was not part of the original team writing the paper, but I am working on the application of dual contouring technique to scoliosis surgery (see the last paragraph of section 2.3).
Regards,
Lucas Potter
############
Thanks Lucas,
This complicates things. It is a paper that adds many elements together. So your work was probably referenced to some degree. Yet your name does not appear in the references quoted in the work like [Rashid] , so I assume your work is relatively new, perhaps corresponding to the last line in the paragraph. Please correct me if I am wrong.
I suspect that your name was added mostly due to presentation constraints. If this was the main reason for adding your name, then it was not necessary. The lab can still send you to present the work without being an author in the paper. The presenter does not have to be an author - although its highly desirable.
However, if you add new material to the paper that describes your recent findings that support the paper, then you can be added as an author. However, this must be done within a day since we are pressing against a deadline that is hard and all the proper documents and forms must be uploaded before June 12 - which also takes time. The other option is removing your name.
So in summary there are two choices to get the paper accepted:
1. Remove your name from the author list.
2. Keep your name and add sufficient material to justify adding your name as an author.
Whatever path you choose should be done quickly with a final version submitted tomorrow.
Hopefully this time table is possible.
Jacob
############
Hi Jacob,
Okay, if it's easier then, I will remove Lucas' name as an author and still direct him to make the presentation. Lucas' contribution coincides more with the future of the project than what has been achieved so far.
Lucas, I will contact you with an expense account with which to plan your travel; I will ask MSVE admin assistant Jayne Massey to help you. Please get familiar with the paper. I will dig up some similar slides as well as ask the other students to also provide you with some. You can easily dig up images from the doc file itself.
My apologies for the false start.
Michel Audette, Ph.D.
Associate Professor,
Department of Modeling, Simulation and Visualization Engineering,
Old Dominion University,
Norfolk, VA.
############
Ok Michel,
This version is acceptable.
You can proceed to final upload. Look at your email - you should have received an automated email of acceptance with a link to the final submission form.
You will need 4 documents:
1. The final pdf manuscript
2.The original that created the pdf - in your case it is the doc format document
3. The copyright firm filled - there are two pages there - make sure you sign both. Here is the link to the form:
http://scs.org/wp-content/uploads/2016/10/AuthorsKitForms-TransferOfCopyrightAuthorCert.pdf
4. A response for reviewers. You can just copy and paste our email conversation that I will make available in the following link in about half an hour:
https://groups.google.com/forum/#!topic/public-scientific-reviews/IxlT5LUpU-w
I do still allow the option of keeping Lucas's name in the last version you upload if some of his latest work is reported as well - beyond what is in the paper now. However, I suggest that you first upload the version you sent me since the hard deadline I was given is June 12th and the authors do not wish to fall on a technicality.
Once you upload, if you want to work more and add a few words about Lucas's newer work to allow him as an author, send me a new version by email and if It is substantial enough and there still time, it may be possible. However, it is awfully close to the deadline and it may be better to leave this for future publication.
Sorry for the less than immediate response, I just saw your message now - for some reason it was not marked as new by my mailer. Hopefully you get it in time.
Jacob
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