Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Publishing in JOSS : Added paper summary for IVIM #1126

Closed
wants to merge 8 commits into from

Conversation

@quantshah
Copy link
Contributor

commented Oct 6, 2016

As per the discussion in #1110 and guidelines given by "The Journal of Open Source Software", I have made the first draft to submit a paper for the ivim module. I think this can be done for others too. JOSS asks for a "paper.md" for publishing and you can find the draft for ivim under "dipy/paper/joss/reconst_ivim/". The idea is that for other modules, one can add new folders accordingly. (dipy/paper/joss/denoise_adaptive_soft_matching/). More details can be found at http://joss.theoj.org

@coveralls

This comment has been minimized.

Copy link

commented Oct 6, 2016

Coverage Status

Coverage remained the same at 83.233% when pulling 7bae817 on sahmed95:joss into c1ba780 on nipy:master.

1 similar comment
@coveralls

This comment has been minimized.

Copy link

commented Oct 6, 2016

Coverage Status

Coverage remained the same at 83.233% when pulling 7bae817 on sahmed95:joss into c1ba780 on nipy:master.

@codecov-io

This comment has been minimized.

Copy link

commented Oct 6, 2016

Current coverage is 80.86% (diff: 100%)

Merging #1126 into master will decrease coverage by 0.29%

@@             master      #1126   diff @@
==========================================
  Files           215        217     +2   
  Lines         24370      24593   +223   
  Methods           0          0          
  Messages          0          0          
  Branches       2448       2491    +43   
==========================================
+ Hits          19780      19888   +108   
- Misses         4084       4194   +110   
- Partials        506        511     +5   

Powered by Codecov. Last update c1ba780...ff4a429

arokem and others added 3 commits Oct 6, 2016
Fix my affiliation, reference format and a few sentences.
Also, removes some weird (non-unicode?) characters.
Merge pull request #3 from arokem/joss-edits
Fix my affiliation, reference format and a few sentences.
@coveralls

This comment has been minimized.

Copy link

commented Oct 7, 2016

Coverage Status

Coverage remained the same at 83.233% when pulling cf248e0 on sahmed95:joss into c1ba780 on nipy:master.

1 similar comment
@coveralls

This comment has been minimized.

Copy link

commented Oct 7, 2016

Coverage Status

Coverage remained the same at 83.233% when pulling cf248e0 on sahmed95:joss into c1ba780 on nipy:master.

@coveralls

This comment has been minimized.

Copy link

commented Oct 8, 2016

Coverage Status

Coverage remained the same at 83.233% when pulling cf248e0 on sahmed95:joss into c1ba780 on nipy:master.

1 similar comment
@coveralls

This comment has been minimized.

Copy link

commented Oct 8, 2016

Coverage Status

Coverage remained the same at 83.233% when pulling cf248e0 on sahmed95:joss into c1ba780 on nipy:master.

@etpeterson

This comment has been minimized.

Copy link
Contributor

commented Oct 12, 2016

Looks pretty good to me. I'm not sure if I did it right, but I tried to make a commit to this, it looks like it ended up here: https://github.com/nipy/dipy/compare/master...etpeterson:patch-1?expand=1

I just added my orcid ID and made a few text changes.

@arokem

This comment has been minimized.

Copy link
Member

commented Oct 12, 2016

I made that into a PR here: quantshah#4, so that @sahmed95 can merge it into this one.

@etpeterson

This comment has been minimized.

Copy link
Contributor

commented Oct 12, 2016

Thanks! How are you supposed to do that so I know for next time?

@arokem

This comment has been minimized.

Copy link
Member

commented Oct 12, 2016

git remote add sahmed95 https://github.com/sahmed95/dipy.git
git fetch sahmed95
git checkout joss
git checkout -b joss-edits-etpeterson #or some-such
# Edit, edit, edit
git commit -a -m"Suggestions and comments"
git push origin joss-edits-etpeterson

Then, go to the Github website. And submit a pull request. When you do
that, use the drop-down menus at the top to select the base fork as
sahmed95 and the based branch as joss. Set the head fork to your fork
and the branch to your joss-edits-etpeterson.

On Wed, Oct 12, 2016 at 9:12 AM, Eric Peterson notifications@github.com
wrote:

Thanks! How are you supposed to do that so I know for next time?


You are receiving this because you commented.
Reply to this email directly, view it on GitHub
#1126 (comment), or mute
the thread
https://github.com/notifications/unsubscribe-auth/AAHPNkLQmLItZzRGhcnZhIb9iQ33VzNuks5qzQbagaJpZM4KP7gU
.

@etpeterson

This comment has been minimized.

Copy link
Contributor

commented Oct 12, 2016

Great, thanks. I (foolishly) thought I found a way to do that web only.

@arokem

This comment has been minimized.

Copy link
Member

commented Oct 12, 2016

I believe you were one click away :-)

Merge pull request #4 from etpeterson/patch-1
Added my orcid and edited the text a little
@coveralls

This comment has been minimized.

Copy link

commented Oct 12, 2016

Coverage Status

Coverage remained the same at 83.233% when pulling ddd38fa on sahmed95:joss into c1ba780 on nipy:master.

1 similar comment
@coveralls

This comment has been minimized.

Copy link

commented Oct 12, 2016

Coverage Status

Coverage remained the same at 83.233% when pulling ddd38fa on sahmed95:joss into c1ba780 on nipy:master.

@arokem

This comment has been minimized.

Copy link
Member

commented Oct 16, 2016

Any more comments here? @RafaelNH : you OK with this?

@RafaelNH

This comment has been minimized.

Copy link
Contributor

commented Oct 16, 2016

Hi guys! So sorry, I completely miss all the notification on this! I will take the afternoon today to work on this!

index: 2
- name: SRI International
index: 3
- name: Cognition and Brain Sciences Unit (CBU)

This comment has been minimized.

Copy link
@RafaelNH

RafaelNH Oct 16, 2016

Contributor

MRC Cognition and Brain Sciences Unit, Cambridge, UK

journal = {Radiology}
}


This comment has been minimized.

Copy link
@RafaelNH

RafaelNH Oct 16, 2016

Contributor

Add following article with lable Le1988ra

Le Bihan, D., Breton, E., Lallemand, D., Aubin, M.L., Vignaud, J., Laval-Jeantet, M. (1988). Separation of Diffusion and Perfusion in Intravoxel Incoherent Motion MR Imaging. Radiology 168(2), 497-505. doi: 10.1148/radiology.168.2.3393671


# Summary

Intra-voxel incoherent motion (IVIM) is a biophysical model that describes diffusion

This comment has been minimized.

Copy link
@RafaelNH

RafaelNH Oct 16, 2016

Contributor

I am being picky here - I will suggest not calling this a biophysical model. One can argue that this is indeed a biophysical model, however I am suggesting to rename this here just to avoid confusions. In general biophysical models only aim to relate the diffusion decay with biological feature (ignoring perfusion). Here the objective is to separate diffusion and perfusion effects. How about replacing the first sentence with the following:

Intra-voxel incoherent motion (IVIM) imaging is a technique that aims to separate effects of perfusion (microcirculation of blood in the capillary network) from the effects of molecular diffusion from the [@le1986mr, @le1988ra].

Intra-voxel incoherent motion (IVIM) is a biophysical model that describes diffusion
and perfusion in the signal acquired with a multi-diffusion value MRI
acquisition [@le1986mr]. This method was originally developed to study the
fast and slow motion of water molecules in the human brain -- an indication of brain

This comment has been minimized.

Copy link
@RafaelNH

RafaelNH Oct 16, 2016

Contributor

How about:

This method was originally developed to study the perfusion and diffusion in the human brain [@le1986mr], but more recently, interest in this technique has expanded ...

@RafaelNH

This comment has been minimized.

Copy link
Contributor

commented Oct 16, 2016

I didn't realize that JOSS only requires a short summary of the technique. Give a look to my suggestions!

@quantshah

This comment has been minimized.

Copy link
Contributor Author

commented Oct 17, 2016

@RafaelNH Can you please add your orcid ? Please have a look at the changes too.

@coveralls

This comment has been minimized.

Copy link

commented Oct 18, 2016

Coverage Status

Coverage decreased (-0.3%) to 82.938% when pulling 0328bbd on sahmed95:joss into c1ba780 on nipy:master.

1 similar comment
@coveralls

This comment has been minimized.

Copy link

commented Oct 18, 2016

Coverage Status

Coverage decreased (-0.3%) to 82.938% when pulling 0328bbd on sahmed95:joss into c1ba780 on nipy:master.

@arokem

This comment has been minimized.

Copy link
Member

commented Oct 21, 2016

@RafaelNH : are you satisfied with the changes?


# Summary

Intra-voxel incoherent motion (IVIM) is a technique that aims to separate effects of perfusion (microcirculation of blood in the capillary network) from the effects of molecular diffusion [@le1986mr, @le1988ra] in the signal acquired with a multi-diffusion value MRI acquisition [@le1986mr]. This method was originally developed to study the perfusion and diffusion in the human brain [@le1986mr], but more recently, interest in this technique has expanded and applications have emerged throughout the body [@LeBihan2008] including kidneys, liver, and heart [@Powers1991, @PMID:9038058, @Callot2003, ]. Many more applications are now under investigation such as cancer imaging (prostate, liver, kidney, pancreas, etc.) [@Koh2011] and imaging of the human placenta [@Moore2000, @moore2000vivo]. One of its most common applications still remains brain mapping for neuroscience research

This comment has been minimized.

Copy link
@RafaelNH

RafaelNH Oct 21, 2016

Contributor

First sentence:
Intra-voxel incoherent motion (IVIM) is a technique that aims to separate effects of perfusion (microcirculation of blood in the capillary network) from the effects of molecular diffusion in MRI images acquired with a multi-diffusion weights [@le1986mr, @le1988ra].

orcid: 0000-0002-3530-9652
affiliation: 3
- name: Rafael Neto Henriques
orcid: 0000-0000-0000-1234

This comment has been minimized.

Copy link
@RafaelNH

RafaelNH Oct 21, 2016

Contributor

0000-0002-3891-8189

@RafaelNH

This comment has been minimized.

Copy link
Contributor

commented Oct 21, 2016

@sahmed95! Please change my orcid to 0000-0002-3891-8189 and the first sentence of the article and this is ready to go for me =).

@quantshah

This comment has been minimized.

Copy link
Contributor Author

commented Oct 21, 2016

If this is okay then the next step is to fill out the submission form with the following details.

Title
Ivim: A model for diffusion and perfusion analysis of MRI

Repository address (Which one do I submit ?)
https://github.com/nipy/dipy/blob/master/dipy/reconst/ivim.py
#1110
https://github.com/nipy/dipy/

Version
Will this be dipy version ?

Description
A reconstruction model that fits a bi-exponential curve to diffusion image data (NiFTI) and gives the 4 parameters S0, f, D* and D for each voxel. The bi-exponential curve is defined in the Intra-voxel incoherent motion model where the signal values are a function of the above parameters and the variable diffusion encoding sensitivities (b­values).

@coveralls

This comment has been minimized.

Copy link

commented Oct 21, 2016

Coverage Status

Coverage decreased (-0.3%) to 82.938% when pulling ff4a429 on sahmed95:joss into c1ba780 on nipy:master.

1 similar comment
@coveralls

This comment has been minimized.

Copy link

commented Oct 21, 2016

Coverage Status

Coverage decreased (-0.3%) to 82.938% when pulling ff4a429 on sahmed95:joss into c1ba780 on nipy:master.

@arokem

This comment has been minimized.

Copy link
Member

commented Oct 21, 2016

I've pinged the JOSS team (at the end of this issue: openjournals/joss#52). Let's see what they say.

@Garyfallidis

This comment has been minimized.

Copy link
Member

commented Jul 15, 2017

Are we still waiting for the JOSS team for this?

@arokem

This comment has been minimized.

Copy link
Member

commented Mar 15, 2019

I believe this one is stale and we're going to try to address publication of this work through other means. Stay tuned. For now, I am closing this one.

@arokem arokem closed this Mar 15, 2019

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
7 participants
You can’t perform that action at this time.