Joss-reviews: [PRE REVIEW]: MiTfAT: A Python-based scikit-learn-friendly fMRI Analysis Tool, Made in Tuebingen.
Submitting author: @vahid-sb (Vahid S. Bokharaie)
Repository: https://github.com/vahid-sb/MiTfAT
Version: v0.1.7
Editor: @arokem
Reviewers: @JonathanReardon, @emdupre
Managing EiC: Kyle Niemeyer
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Author instructions
Thanks for submitting your paper to JOSS @vahid-sb. Currently, there isn't an JOSS editor assigned to your paper.
The author's suggestion for the handling editor is @arokem.
@vahid-sb if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).
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All 32 comments
Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.
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Software report (experimental):
github.com/AlDanial/cloc v 1.84 T=0.11 s (177.2 files/s, 31494.2 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 17 504 1023 1870
reStructuredText 1 39 7 54
Markdown 1 21 0 36
YAML 1 0 0 1
-------------------------------------------------------------------------------
SUM: 20 564 1030 1961
-------------------------------------------------------------------------------
Statistical information for the repository 'ae544ff2e67d943433bc2cd6' was
gathered on 2020/10/24.
The following historical commit information, by author, was found:
Author Commits Insertions Deletions % of changes
Vahid Bokharaie 7 4095 698 100.00
Below are the number of rows from each author that have survived and are still
intact in the current revision:
Author Rows Stability Age % in comments
Vahid Bokharaie 3397 83.0 0.0 14.84
PDF failed to compile for issue #2778 with the following error:
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whedon
on 24 Oct 2020
Hi @vahid-sb, it looks like the header of your paper may not be valid鈥攑lease take a look at the example paper. It may just be missing the --- line to close the YAML header section.
Also, your reference(s) should be contained in a .bib file, rather than hardcoded in the paper.
kyleniemeyer
on 24 Oct 2020
@arokem could you edit this submission?
kyleniemeyer
on 24 Oct 2020
@whedon invite @arokem as editor
kyleniemeyer
on 24 Oct 2020
@arokem has been invited to edit this submission.
whedon
on 24 Oct 2020
Hi @vahid-sb, it looks like the header of your paper may not be valid鈥攑lease take a look at the example paper. It may just be missing the
---line to close the YAML header section.Also, your reference(s) should be contained in a .bib file, rather than hardcoded in the paper.
HI @kyleniemeyer, both issues are resolved now. Thanks for drawing my attention to them. Seems I deleted '---' after the header. Didn't know it is part of .md file commands. Also, reference is now read from a bib file.
vahid-sb
on 24 Oct 2020
@whedon generate pdf
kyleniemeyer
on 25 Oct 2020
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
whedon
on 25 Oct 2020
@vahid-sb thanks, looks good now. I'll wait on @arokem to (hopefully) take over soon and identify reviewers.
kyleniemeyer
on 25 Oct 2020
Yeah. I can take this one.
arokem
on 26 Oct 2020
@whedon assign arokem as editor
arokem
on 26 Oct 2020
OK, the editor is @arokem
whedon
on 26 Oct 2020
馃憢 @snastase : Would you be willing to review this article for JOSS?
arokem
on 26 Oct 2020
馃憢 @JonathanReardon : Would you be willing to review this article for JOSS?
arokem
on 26 Oct 2020
Hi @arokem, I'm happy to review this -- looks like a nice project. When would you want it completed by?
JonathanReardon
on 26 Oct 2020
@vahid-sb : while we are waiting for reviewers to come on-board, a few comments from me:
- There are several other software libraries that do things that are closely related to what MiTfAT does. For example, nilearn. I think that you will need to add a section to your paper describing previous similar work and describing the relationship between the present library and this previous work.
- The word "Neuroscience" (first line) should not be capitalized.
- "belts and whistles" should be "bells and whistles". I should also add that I don't understand exactly what this sentence means. It seems to suggest that MiTfAT is somehow simpler to use than other software, but provides little evidence to support this assertion. I would rethink how you would like to say this in a manner that emphasizes design choices made by different libraries, rather than posing this as an assertion.
- Though novelty per-se is not a requirement, the text does imply that MiTfAT implements novel methods. What are these analysis methods?
- The word "accomponied" should be spelled "accompanied".
arokem
on 26 Oct 2020
@JonathanReardon : thanks for your quick response here! We usually aim to finish all parts of the review within six weeks, so if you think that you could turn around comments in two-three weeks, that would be ideal.
arokem
on 26 Oct 2020
@whedon add @JonathanReardon as reviewer
arokem
on 26 Oct 2020
OK, @JonathanReardon is now a reviewer
whedon
on 26 Oct 2020
@JonathanReardon : thanks for your quick response here! We usually aim to finish all parts of the review within six weeks, so if you think that you could turn around comments in two-three weeks, that would be ideal.
Yes, absolutely fine! thanks
JonathanReardon
on 26 Oct 2020
@vahid-sb : while we are waiting for reviewers to come on-board, a few comments from me:
* There are several other software libraries that do things that are closely related to what MiTfAT does. For example, [nilearn](https://nilearn.github.io/). I think that you will need to add a section to your paper describing previous similar work and describing the relationship between the present library and this previous work. * The word "Neuroscience" (first line) should not be capitalized. * "belts and whistles" should be "bells and whistles". I should also add that I don't understand exactly what this sentence means. It seems to suggest that MiTfAT is somehow simpler to use than other software, but provides little evidence to support this assertion. I would rethink how you would like to say this in a manner that emphasizes design choices made by different libraries, rather than posing this as an assertion. * Though novelty per-se is not a requirement, the text does imply that MiTfAT implements novel methods. What are these analysis methods? * The word "accomponied" should be spelled "accompanied".
Thanks, @arokem, and thanks @JonathanReardon for agreeing to review.
@arokem I have updated the paper correcting the typos you kindly reminded me of. About Nilearn, I am aware of that and it is one of the requirements for mitfat, although I have used it merely for IO operations. But mitfat treats the data in a more comprehensive manner, not simply as separate NumPy arrays that might or might not be related. I have defined a class for fMRI data which is the cornerstone of the code. I added a short description of that to the paper. And about novelty, it is true that what I was looking for, I could find in the common fMRI analysis packages, but that does not mean the methods themselves are new. Simply smart applications of undergraduate mathematics, that's how I would characterize them. For example, the detrending method discussed in Chapter 8 of the manual.
vahid-sb
on 26 Oct 2020
Apologies if this is a mistake my end, but has the review process started yet? it's not showing as started my end. Also, am I the only person reviewing? Thanks.
JonathanReardon
on 9 Nov 2020
Thanks for checking. The review process has not started yet. I still need to find one more reviewer but I have been somewhat distracted in the last week or so.
arokem
on 9 Nov 2020
:wave: @emdupre : would you be willing to review this article for JOSS?
arokem
on 9 Nov 2020
Thanks for checking. The review process has not started yet. I still need to find one more reviewer but I have been somewhat distracted in the last week or so.
No problem at all, just wanted to be sure.
JonathanReardon
on 9 Nov 2020
Yes, I'd be happy to review ! Let me know what I can do at this point to help in that process.
emdupre
on 9 Nov 2020
@whedon add @emdupre as reviewer
arokem
on 9 Nov 2020
OK, @emdupre is now a reviewer
whedon
on 9 Nov 2020
@whedon start review
arokem
on 9 Nov 2020
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2827.
whedon
on 9 Nov 2020
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