Paper: Numerical simulation of liver perfusion: from CT scans to FE model (V. Lukeš)

[pdebuyl]

Dear Vladimir,

Thanks for your submission. Reviewing will take place here after 20 august.

Regards, Pierre

[rougier]

@pdebuyl @NelleV I will review the paper.

[rougier]

Review

This paper presents the numerical simulation of liver perfusion motivated by surgeons demand for better tools. The paper is well-written and structured (introduction, volumetric model, geometric model, mathematical model, conclusion) and provides just enough details for a non-specialist to understand the complexity of the problem.

Major Comments

• Authors uses a lot of python tools (pyqt, pyvtk, sfepy, pydicom) but no details are provided (but the references), this makes a bit difficult to understand the overall approach for reader unfamiliar with the domain. I think a section giving an overview of the approach would definitely help the reader as well as a figure introducing the architecture.
• Even if references are given, it would be good to explain the status of the processing toolchain. Is it available somewhere if someone wants to use it for a similar problem ? Is is open source ? An explicit url address would be nice.

• There is no state of the art for other approaches

  • do they exist ?
  • what kind of tools ?
  • why don't they suit authors' need ?
  • what about other organs (maybe dumb question sorry, i'm not from the domain)

  I think a state of the art (even short) would help authors in promoting their work.

• Figure 6 is hard to understand and caption does not really help.
• Conclusion: since you introduced surgeons need for such tool, I wonder if this is already used or experimented by surgeons ? Or is the parameter tuning the current barrier ?

Minor comments

• "The code is written mostly in Python" What are the other languages/frameworks ?
• Figure 3 caption might welcome a few more details (where does this screenshot come from ?)
• Figure 4 caption. What are the difference between the 4 figures ? (different hierarchies is not very explicit)
• Figure 7 what is the difference between left and right ?
• Figure 8: Nice, but it might be better to have a full width figure, clearly separating time 3.5 and 22.0
• [Jir] link does not work
• [Kol] link not colored
• [Luk] link cut (redirect to sfepy, not pydicom)
• [Mül] link not colored

[vlukes]

Thank you for the review and comments. I will try to improve the paper within a week.

Regards, Vladimir

[dalcinl]

There is not too much left to say after the careful review of @rougier. I would like to add the following list of suggestions:

• Section 2.1, 1st. paragraph: Consider replacing big -> large in big individual anatomy differences.
• Section 2.1, 2nd. paragraph: Consider spelling Python with initial upper-case in the python wrapper by Andreas Müller.
• Section 2.2, 1st. and 2nd. paragraphs: Consider spelling Marching cubes, that is, cubes in plural.
• Section 4, 3rd. paragraph: Consider removing the word somehow.
• Section 4.1, 1st paragraph: I would remove the quotation marks from 1D and 3D.

[pdebuyl]

Dear @rougier and @dalcinl , thank you for your reviews.

As Davide @vlukes has updated the manuscript, may you confirm that the updates address satisfactorily your reviews?

Thanks, Pierre

[rougier]

Where is the pdf, I cannot find it...

[pdebuyl]

Hi, it's back at http://pdebuyl.be/tmp/esp2014_draft.pdf , sorry.

[rougier]

Yes, mush much better now, only a few minor comments:

• Figure 1: block LISA and DICOM2FEM, I get "Py t" (instead of "Python" I imagine)
• Figure 2: If I understood well, it might be worth mentioning green and red areas are done by the surgeon in the caption as well.
• Style of citation is not uniform (3 letters + 2 digits, 3 letters, 2 letters, capital or not etc.) Maybe there is an official style.
• "of (5)-(6)" -> "of (5) and (6)" maybe (not really a range)

Last comment is for the LISA and dicom2fem links which are kind of "hidden" in the figure 1 and references. Since they are central pieces in this work, it would be nice to find a way to better highlight them.

Apart these minor comments, it's good to me.

[dalcinl]

All my suggestions were incorporated.

Regarding @rougier 's comment on citation style, I noticed that the other papers don't use the same style either. I would suggest to use something [Smith14], i.e. full last name and last two digits year, but this change should be also implemented in the other articles.

[pdebuyl]

Thanks all for the updates.

@dalcinl good remark, we did not request explicitly a citation style. It is expected that authors follow the example in papers/00_vanderwalt/00_vanderwalt.rst but not mentioned in the instructions.

[rougier]

Good for me now.

[vlukes]

Thanks all for the comments and suggestions.

Two remarks:

• I can not reproduce the problem in Fig. 1: "Py t" instead of "PyQt" (Linux Mint17: Okular, Acroread, Firefox built-in reader)
• It would be nice to have more citations in the example (papers/00_vanderwalt/00_vanderwalt.rst) to follow them.

[rougier]

@vlukes Nevermind, it's probably my PDF reader that messed it up.

[dalcinl]

@vlukes @rougier I can reproduce the "Py t" issue in Fig. 1 using both the Acrobat Reader app and the Preview app in my Mac running OS X 10.9.4. Also, I had the same issue with the Evince viewer from Fedora 20. Interestingly, when using the Preview app, doing a select+copy+paste, the clipboard seems to get the PyQt string.

[pdebuyl]

Thanks all for the work. I cannot reproduce the issue in Fig. 1 either.

There will layout etc checks before merging the PR though.