Joss-reviews: [PRE REVIEW]: QMRTools: a mathematica toolbox for quantitative MRI analysis
Submitting author: @mfroeling (Martijn Froeling)
Repository: https://github.com/mfroeling/QMRITools
Version: v2.0
Editor: @cMadan
Reviewers: @grlee77, @JoshKarpel
Author instructions
Thanks for submitting your paper to JOSS @mfroeling. The JOSS editor (shown at the top of this issue) will work with you on this issue to find a reviewer for your submission before creating the main review issue.
@mfroeling if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.
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whedon
on 5 Jan 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1154 with the following error:
Can't find any papers to compile :-(
whedon
on 5 Jan 2019
@whedon commands
mfroeling
on 7 Jan 2019
Here are some things you can ask me to do:
# List Whedon's capabilities
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# Compile the paper
@whedon generate pdf
@whedon generate pdf
mfroeling
on 7 Jan 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1154 with the following error:
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon.rb:69:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:32:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:52:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:113:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
whedon
on 7 Jan 2019
@whedon generate pdf
mfroeling
on 7 Jan 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1154 with the following error:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 15 0 15 0 0 145 0 --:--:-- --:--:-- --:--:-- 147
[WARNING] Could not convert image '/tmp/tex2pdf.118/e4c024bc84d042324fc3253cdcf0eab2cad60748.shtml': Cannot load file
Jpeg Invalid marker used
PNG Invalid PNG file, signature broken
Bitmap Invalid Bitmap magic identifier
GIF Invalid Gif signature :
HDR Invalid radiance file signature
Tiff Invalid endian tag value
TGA not enough bytes
Error producing PDF.
! LaTeX Error: Cannot determine size of graphic in /tmp/tex2pdf.118/e4c024bc84d
042324fc3253cdcf0eab2cad60748.shtml (no BoundingBox).
See the LaTeX manual or LaTeX Companion for explanation.
Type H
...
l.260 ...bc84d042324fc3253cdcf0eab2cad60748.shtml}
Looks like we failed to compile the PDF
whedon
on 7 Jan 2019
@whedon generate pdf
mfroeling
on 7 Jan 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1154 with the following error:
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon.rb:69:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:32:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:52:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:113:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
whedon
on 7 Jan 2019
@whedon generate pdf
mfroeling
on 7 Jan 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1154 with the following error:
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon.rb:69:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:32:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:52:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:113:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
whedon
on 7 Jan 2019
@whedon generate pdf
mfroeling
on 7 Jan 2019
Attempting PDF compilation. Reticulating splines etc...
@whedon generate pdf
mfroeling
on 7 Jan 2019
Attempting PDF compilation. Reticulating splines etc...
PDF failed to compile for issue #1154 with the following error:
/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon.rb:83:in check_fields': Paper YAML header is missing expected fields: date (RuntimeError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon.rb:69:ininitialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:32:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/lib/whedon/processor.rb:32:inset_paper'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:52:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/command.rb:27:inrun'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor.rb:387:indispatch'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.0/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-50d5912cf72a/bin/whedon:113:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in
whedon
on 7 Jan 2019
@whedon generate pdf
mfroeling
on 7 Jan 2019
Attempting PDF compilation. Reticulating splines etc...
馃憢 @cMadan - are you willing to edit this submission?
danielskatz
on 7 Jan 2019
@danielskatz - sure, would be happy to
cMadan
on 8 Jan 2019
@whedon assign @cMadan as editor
cMadan
on 8 Jan 2019
OK, the editor is @cMadan
whedon
on 8 Jan 2019
@mfroeling your paper title differs from your repository title. Is this intentional?
Kevin-Mattheus-Moerman
on 8 Jan 2019
@mfroeling your paper title differs from your repository title. Is this intentional?
@Kevin-Mattheus-Moerman no it was not it will be fixed in the next commit.
mfroeling
on 8 Jan 2019
@cMadan other prefered mathematica language reviewers are taqtiqa-mark, rljacobson, acolum, chlalanne, JoshKarpel, wspr
mfroeling
on 8 Jan 2019
@cmadan these also seem suitable reviewers (people I contacted for https://github.com/openjournals/joss-reviews/issues/889) nnadeau, davidnsousa, markus-nilsson, JianCheng
Kevin-Mattheus-Moerman
on 8 Jan 2019
@whedon generate pdf
mfroeling
on 9 Jan 2019
Attempting PDF compilation. Reticulating splines etc...
@nnadeau @markus-nilsson @acolum @JoshKarpel, would you be interested and available to review this submission? Thank you for your consideration!
@Kevin-Mattheus-Moerman, thanks for the additional suggestions!
cMadan
on 9 Jan 2019
@cMadan Would be happy to, although I don't know anything about MRI/QMR so I won't be able to address any related technical concerns.
JoshKarpel
on 9 Jan 2019
@cMadan, unfortunately I am not available at this time.
nnadeau
on 9 Jan 2019
@cMadan Thank you for tagging me, but I'm also not available at this time.
acolum
on 9 Jan 2019
@JoshKarpel, thanks for letting me know! I might still include you as a reviewer, depending who else we get (e.g., someone who knows MRI well but not Mathematica).
@nnadeau @acolum, no problem, thank you for considering!
cMadan
on 10 Jan 2019
Thanks for asking -- unfortunately not available at the moment
markus-nilsson
on 16 Jan 2019
@markus-nilsson, thank you for considering!
@mfroeling, could you tag a few other people you think may be able/interested in reviewing your submission?
cMadan
on 17 Jan 2019
@JianCheng are you available to review my submission since you have expertise in diffusion processing.
@grlee77 are you available to review my submission since you are one of the few reviewers in the list with MRI expertise.
@rljacobson are you available to review my submission as a Mathematica programmer
mfroeling
on 18 Jan 2019
I can take a look. I do have quantitative MRI experience, but I don't have a Mathematica license and have only minimal Mathematica experience (I used it a little as a student).
grlee77
on 18 Jan 2019
@mfroeling I am definitely qualified to review Mathematica code and general computer vision applications, though I do not have specific expertise with MRI imaging. I do not have any expertise in medicine, but I am quite familiar with the mathematical underpinnings of MRI if that helps. (I am a mathematician and computer scientist by training.) Because I start teaching quite soon, my available time is limited. If you are willing to wait ~3 weeks for a completed review, I am willing to review it for you. (The guidelines suggest 2 weeks is more typical.)
Incidentally, I know a computer vision expert with extensive experience with medical imaging who also happens to be a Mathematica expert. I can give him a ping and see if he's interested if that would be helpful. On the other hand, if @grlee77 or @JianCheng are available and have the particular domain-specific expertise, then together we would have both the software/mathematical aspect and the domain-specific aspect of the software covered.
rljacobson
on 19 Jan 2019
@rljacobson thanks for the reply, there is no rush with the review. If you could also give a ping to the computer vision expert that would be great. The more reviewers that can evaluate the toolbox the better in my opinion. Mathematica experts in the field of MR are hard to find ;)
mfroeling
on 21 Jan 2019
@mfroeling Unfortunately, my computer vision expert had to decline. I'll try to be expedient.
rljacobson
on 23 Jan 2019
@grlee77 @JoshKarpel @rljacobson, I think, between the three of you, there is sufficient expertise to review this submission. Let me know if you're good with this plan and I'll start the review.
cMadan
on 24 Jan 2019
@cMadan sounds good to me!
JoshKarpel
on 24 Jan 2019
sounds good to me as well
grlee77
on 24 Jan 2019
@whedon add @grlee77 as reviewer
cMadan
on 26 Jan 2019
OK, @grlee77 is now a reviewer
whedon
on 26 Jan 2019
@whedon add @JoshKarpel as reviewer
cMadan
on 26 Jan 2019
OK, @JoshKarpel is now a reviewer
whedon
on 26 Jan 2019
@rljacobson and others tagged earlier, if you're still interested in reviewing this submission, please let me know. This work is at the intersection of a topic and programming language that don't often overlap, so adequate reviewing will likely include people who cover only part of the project's content--though I also wouldn't want there to be too many reviewers.
I'm going to start the actual review now, but can still add an additional reviewer if someone has time and interest, and would lead to a better project when it gets accepted.
cMadan
on 26 Jan 2019
@whedon start review
cMadan
on 26 Jan 2019
OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1204. Feel free to close this issue now!
whedon
on 26 Jan 2019
@cMadan I'm sorry, I missed this notification. Yes, I am happy to review this submission. You are welcome to add me to #1204 if you wish.
rljacobson
on 27 Jan 2019
@rljacobson, no worries, thank you! I'll go ahead and add you as a reviewer :)
cMadan
on 27 Jan 2019
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