[REVIEW]: qMRLab: Quantitative MRI Analysis, under one umbrella

whedon commented 4 years ago

Submitting author: @agahkarakuzu (Agah Karakuzu) Repository: https://github.com/qMRLab/qMRLab Version: v.2.4.1 Editor: @Kevin-Mattheus-Moerman Reviewer: @grlee77, @mfroeling, @62442katieb Archive: 10.5281/zenodo.4012104

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Review checklist for @grlee77

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@agahkarakuzu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @mfroeling

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@agahkarakuzu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @62442katieb

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@agahkarakuzu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @grlee77, @mfroeling, @62442katieb it looks like you're currently assigned to review this paper :tada:.

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Kevin-Mattheus-Moerman commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

PDF failed to compile for issue #2343 with the following error:

sh: 0: getcwd() failed: No such file or directory pandoc: 10.21105.joss.02343.pdf: openBinaryFile: does not exist (No such file or directory) Looks like we failed to compile the PDF

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.21105/joss.00656 may be missing for title: QUIT: QUantitative imaging tools
- https://doi.org/10.1016/b978-012372560-8/50002-4 may be missing for title: Statistical parametric mapping
- https://doi.org/10.1101/343079 may be missing for title: Let’s talk about cardiac T1 mapping
- https://doi.org/10.1016/j.softx.2019.100369 may be missing for title: Total Mapping Toolbox (TOMATO): An open source library for cardiac magnetic resonance parametric mapping
- https://doi.org/10.5210/fm.v3i2.578 may be missing for title: The cathedral and the bazaar

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 4 years ago

@grlee77, @mfroeling, @62442katieb this is where the review takes place. Please read the above instructions :point_up: (including suggestions on preventing unwanted GitHub notifications).

You each have a set of checkboxes to guide you through the review process. It would be great if you could review this work in about 2 weeks. Although we can be flexible regarding review time (especially during these challenging times!!!) it would be great if you would let us know if you need more time.

Thanks again for your help!!!! Let the reviewing begin :tada: :robot: :rocket:

Kevin-Mattheus-Moerman commented 4 years ago

@grlee77, @mfroeling, @62442katieb thanks again for your help with this review. I see @mfroeling has started. @grlee77, @62442katieb how are you getting on? Let me know if you have questions.

grlee77 commented 4 years ago

Hey all, sorry about the delay. I will review this over the next day or so.

grlee77 commented 4 years ago

@Kevin-Mattheus-Moerman, can you please resend the invitation?

When I click the link to accept it in the first comment it says it is expired (so I am unable to edit the checklist).

danielskatz commented 4 years ago

@whedon re-invite @grlee77 as reviewer

whedon commented 4 years ago

OK, the reviewer has been re-invited.

@grlee77 please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

grlee77 commented 4 years ago

Re: Contributions and authorship item

Can the authors clarify briefly how authorship criteria were decided? I see that most authors overlap with the repository's significant source code contributors, but I understand contributions can also come in other forms. Two authors I don't see an obvious alias for in the commit history are Drs. Pike and Stikov. Also, there appear to be a few significant contributors (e.g. 30+ commits) who do not appear in the author list (although it is hard to tell for sure based on GitHub handles).

grlee77 commented 4 years ago

Re: installation instructions item:

Your documentation for this is good, but it would be nice if you also listed which commercial Matlab toolboxes are required. I saw that for Octave, specific toolboxes were listed.

FWIW, I ran a few of the demos and then typed license('inuse') and saw

image_toolbox
matlab
optimization_toolbox

but I did not run everything, so there may be others as well.

grlee77 commented 4 years ago

Please double-check the formatting of the references. For example the first reference (SPM) seems to be incomplete and the Weiskopf et. al. reference has a stray "Citeseer" listed.

grlee77 commented 4 years ago

Re: citations:

The authors cite several relevant packages, but one area that does not seem to be represented is for Diffusion MRI. qMRLab does provide DTI, CHARMED and NODDI functionality, so it seems relevant to cite some packages in this area as well. Some common tools for that are free, but not open source, but a few open source ones I am aware of are:

DIPY and DMIPY (Python) (full disclosure: I have been an occasional DIPY contributor) Camino (Java) DSI Studio (C++)

Of course, it will not be possible to cite everything, but 1-2 sentences regarding other open-source diffusion processing tools would be nice.

grlee77 commented 4 years ago

Regarding the included figure, it is pretty, but I wonder if there is any issue on JOSS's end to publish a figure including logos of other packages like Matlab, Docker, Plotly, etc. When we submitted the SciPy paper (albeit not for JOSS), there were originally various logos in a historical timeline figure, but the editorial team required the removal of any copyrighted logos prior to publication.

Also, when performing this review, I have only reviewed qMRLab itself, but did not evaluate the related projects like qMRFlow, etc. I think it is appropriate to mention these related projects in the text, but I don't think the figure needs to include them. I guess what I am saying is that the figure looks a bit more like an advertisement for the broader software eco-system surrounding qMRLab and should perhaps be a bit more narrowly focused on the quantitative mapping subset described in the publication.

@Kevin-Mattheus-Moerman: can you advise on any potential issues regarding logos on JOSS's end?

Kevin-Mattheus-Moerman commented 4 years ago

Regarding the included figure, it is pretty, but I wonder if there is any issue on JOSS's end to publish a figure including logos of other packages like Matlab, Docker, Plotly, etc. When we submitted the SciPy paper (albeit not for JOSS), there were originally various logos in a historical timeline figure, but the editorial team required the removal of any copyrighted logos prior to publication.

Also, when performing this review, I have only reviewed qMRLab itself, but did not evaluate the related projects like qMRFlow, etc. I think it is appropriate to mention these related projects in the text, but I don't think the figure needs to include them. I guess what I am saying is that the figure looks a bit more like an advertisement for the broader software eco-system surrounding qMRLab and should perhaps be a bit more narrowly focused on the quantitative mapping subset described in the publication.

@Kevin-Mattheus-Moerman: can you advise on any potential issues regarding logos on JOSS's end?

@grlee77 thanks for raising this issue with us. The logos are acceptable.

Kevin-Mattheus-Moerman commented 4 years ago

@agahkarakuzu can you respond to the comments by @grlee77 ?

62442katieb commented 4 years ago

Re: Contributions and authorship item

Can the authors clarify briefly how authorship criteria were decided? I see that most authors overlap with the repository's significant source code contributors, but I understand contributions can also come in other forms. Two authors I don't see an obvious alias for in the commit history are Drs. Pike and Stikov. Also, there appear to be a few significant contributors (e.g. 30+ commits) who do not appear in the author list (although it is hard to tell for sure based on GitHub handles).

I would also like clarification on the authorship decisions. Thanks!

agahkarakuzu commented 4 years ago

@grlee77 @62442katieb

Re: Contributions and authorship item

Two authors I don't see an obvious alias for in the commit history are Drs. Pike and Stikov.

Bruce Pike and Nikola Stikov (my advisor) are principal investigators of the research labs funding our project

Can the authors clarify briefly how authorship criteria were decided?

For the authorship, we thought maintainers, active contributors and PIs fit for the authorship. These are the contributors regularly joining our bi-weekly meetings. For clarity, below is a brief breakdown of authorship roles:
- Agah Karakuzu: Maintainer, improved the qMRLab framework, significant contributions to the codebase, added DevOps and new qMRI models, wrote the manuscript.
- Mathieu Boudreau: Maintainer, significant contributions to the codebase, added new qMRI models, revised the manuscript
- Tanguy Duval: Former maintainer, created qMRLab framework based on qMTLab, significant contributions to the codebase, revised the manuscript
- Tommy Boshkovski: Active contributor, added qMRI models, helped improve documentation, created the web portal, revised the manuscript.
- Ilana R. Leppert: Active contributor, added qMRI models, revised the manuscript.
- Bruce Pike: Principal Investigator, contributed funds for the development of the software, revised the manuscript.
- Julien Cohen-Adad: Principal Investigator, contributions to the codebase, contributed funds for the development of the software, provided valuable insights on software development, revised the manuscript.
- Nikola Stikov: Principal Investigator, main supervisor of the project and academic supervisor of A.K. and T.B., contributed funds for the development of the software, revised the manuscript

Also, there appear to be a few significant contributors (e.g. 30+ commits) who do not appear in the author list (although it is hard to tell for sure based on GitHub handles).

I would like to note that later on in the project, we started using squash and merge option to merge the commits into the master. Therefore, at least for this codebase, number of commits is not necessarily an objective measure of the relative code contributions. Nonetheless, we are more than happy to welcome all the contributors as authors if the JOSS policy (@Kevin-Mattheus-Moerman ) requires and/or the reviewers @grlee77 @62442katieb strongly recommend to do so.

Also, when performing this review, I have only reviewed qMRLab itself, but did not evaluate the related projects like qMRFlow, etc. I think it is appropriate to mention these related projects in the text, but I don't think the figure needs to include them.

Thank you @grlee77, I agree with your point. I will update the figure to confine the content to qMRLab codebase only and simplify it.

[x] The comment will be addressed in the revised manuscript.

The authors cite several relevant packages, but one area that does not seem to be represented is for Diffusion MRI. qMRLab does provide DTI, CHARMED and NODDI functionality, so it seems relevant to cite some packages in this area as well.

Thank you for the suggestion. I agree that including some open source examples from the Diffusion MRI field is relevant.

[x] The comment will be addressed in the revised manuscript.
[x] Please double-check the formatting of the references.
[x] it would be nice if you also listed which commercial Matlab toolboxes are required

Thank you so much @grlee77 for your valuable comments, I will soon address them and make a PR.

agahkarakuzu commented 4 years ago

@Kevin-Mattheus-Moerman I responded to the comments by @grlee77 and @62442katieb and addressed the issues raised in qMRLab PR #399 (joss_rev1 into master).

I compiled the PDF from the joss_rev1 branch, available here. Not sure about longevity of this link, but this should help reviewers until whedon builds one for us.

grlee77 commented 4 years ago

I would like to note that later on in the project, we started using squash and merge option to merge the commits into the master. Therefore, at least for this codebase, number of commits is not necessarily an objective measure of the relative code contributions. Nonetheless, we are more than happy to welcome all the contributors as authors if the JOSS policy (@Kevin-Mattheus-Moerman ) requires and/or the reviewers @grlee77 @62442katieb strongly recommend to do so.

Agreed, Re: commits not being an ideal measure of effort. I'm not sure in regards to JOSS policy, but given that it only seems to be a few additional contributors, it shouldn't be much work to invite them. I prefer to lean toward the side of being more inclusive rather than less. If they are uninterested or you do not receive a timely response, then do not include them among the primary authors, perhaps just adding a generic acknowledgement of the contributions of "qMRLab community contributors".

Kevin-Mattheus-Moerman commented 4 years ago

@agahkarakuzu @grlee77 In relation to authorship here is our policy on this: https://joss.readthedocs.io/en/latest/submitting.html#authorship. In short "The authors themselves assume responsibility for deciding who should be credited with co-authorship, and co-authors must always agree to be listed.", In this case some contributors were identified which perhaps could be added as authors. I leave this decision with @agahkarakuzu. If this concerns a small amount of contributors, and you do not mind, then I do suggest inviting them (if their contributions are sufficient enough) to see if they feel they would like to be added as a co-author here.

Kevin-Mattheus-Moerman commented 4 years ago

@mfroeling any updates on your end? How are you getting on with this review? Thanks.

agahkarakuzu commented 4 years ago

@Kevin-Mattheus-Moerman thanks for the clarification re authorship, I will discuss this with the team and come up with a time efficient strategy.

grlee77 commented 4 years ago

It looks like qMRLab/qMRLab#399 addresses all of my other comments (the new figure looks good!). Thanks @agahkarakuzu for the quick update.

agahkarakuzu commented 4 years ago

@grlee77 regarding authorship, we will send all the contributors an email and ask if they would like to be co-author. We will wait for a week to collect the responses and the necessary information, then update the author list.

Kevin-Mattheus-Moerman commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.21105/joss.00656 may be missing for title: QUIT: QUantitative imaging tools
- https://doi.org/10.1016/b978-012372560-8/50002-4 may be missing for title: Statistical parametric mapping
- https://doi.org/10.1101/343079 may be missing for title: Let’s talk about cardiac T1 mapping
- https://doi.org/10.1016/j.softx.2019.100369 may be missing for title: Total Mapping Toolbox (TOMATO): An open source library for cardiac magnetic resonance parametric mapping
- https://doi.org/10.4135/9781412950657.n33 may be missing for title: The cathedral and the bazaar

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 4 years ago

@agahkarakuzu can you check those missing DOI's? :point_up:

Kevin-Mattheus-Moerman commented 4 years ago

@grlee77 just had a look at your unchecked boxes. "References" and "Contribution/authorship" are being dealt with. Can you summarize why "State of the field" is unchecked? Thanks!

Kevin-Mattheus-Moerman commented 4 years ago

@mfroeling how are you getting on with this review? Let me know if you have any questions.

grlee77 commented 4 years ago

@grlee77 just had a look at your unchecked boxes. "References" and "Contribution/authorship" are being dealt with. Can you summarize why "State of the field" is unchecked? Thanks!

State of the field was also addressed in their PR (discussion of existing diffusion-related software was added). I wasn't sure if I should wait until it was merged to check them off, but have gone ahead and checked them now so I don't hold up the review.

agahkarakuzu commented 4 years ago

@grlee77 I sent contributors an email and waited for a week for their response. Now I will add those accepted co-authorship in the PR and then merge.

agahkarakuzu commented 4 years ago

@Kevin-Mattheus-Moerman I added missing dois manually (added doi field(s) in paper.bib), I checked them one by one and they all resolve correctly. Now they appear in the refs:

If this looks OK, I will merge the PR to master.

Kevin-Mattheus-Moerman commented 4 years ago

Looks good. Perhaps merge and run @whedon generate pdf and @whedon check references here.

agahkarakuzu commented 4 years ago

@whedon generate pdf

agahkarakuzu commented 4 years ago

@whedon check references

whedon commented 4 years ago

PDF failed to compile for issue #2343 with the following error:

Could not find bibliography file: paper.bib Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.21105/joss.00656 is OK
- 10.1016/b978-012372560-8/50002-4 is OK
- 10.1101/343079 is OK
- 10.1016/j.softx.2019.100369 is OK
- 10.4135/9781412950657.n33 is OK

MISSING DOIs

- https://doi.org/10.1038/nbt.3820 may be missing for title: Nextflow enables reproducible computational workflows
- https://doi.org/10.1101/631952 may be missing for title: TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity
- https://doi.org/10.3389/fninf.2014.00008 may be missing for title: Dipy, a library for the analysis of diffusion MRI data
- https://doi.org/10.3389/fninf.2019.00064 may be missing for title: The dmipy toolbox: Diffusion mri multi-compartment modeling and microstructure recovery made easy

INVALID DOIs

- None

mfroeling commented 4 years ago

@agahkarakuzu My appologies for the delay. I was a bit bussy and needed to find a matlab version with the correct toolboxes which in our IT department had a bit of a delay.

some issues that I think need to be solved.

[ ] When the toolbox starts it needs a check if the needed Matlab dependencies are installed. The first few tries I had issues during data processing that were due to missing or badly installed packages. Especially for the missing packages, there should be a strong warning when starting the toolbox that it will not run properly.
[ ] Example data is provided for the T1 relaxometry in the documentation. After some browsing the GUI I found the download example button also for other modalities. This should be better documented. I started with the command line and there I could not find a list of available example data.
[ ] Each model needs a specific data setup that is apparently inferred from the files in the folder. One can load each data needed separately or by selecting the containing folder. However, for me, it is not clear how the data structure/naming should be for every type of data supported if one wants to used the predefined data format. For example, when additional data quantitative data is loaded how should this be stored (e.g. B1 can be fraction or percent).
[ ] I loaded one of my own diffusion sets and the bval/bvec files were not loaded or asked for. without this information the tool still allowed me to click the fit button resulting in errors. Only after some exploration I found the load bval/bvec in the options pannel. Nowhere in the help of the diffusion does it state that I have to load my own bval/bvec files.
[ ] different models ask for different input files. This is nicely provided in the GUI however I would be nice if mandatory and optional inputs would be clear. For example, with DTI processing I don't need a mask or SigmaNoise to be able to fit a Tensor.
[ ] When I loaded the example diffusion data and then changed the input to one of my own datasets the mask of the previous dataset remained in the Mask input field only after clicking browse and cancel is was cleared.

Kevin-Mattheus-Moerman commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 4 years ago

@whedon check references

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.21105/joss.00656 is OK
- 10.1016/b978-012372560-8/50002-4 is OK
- 10.1101/343079 is OK
- 10.1016/j.softx.2019.100369 is OK
- 10.4135/9781412950657.n33 is OK

MISSING DOIs

- https://doi.org/10.1038/nbt.3820 may be missing for title: Nextflow enables reproducible computational workflows
- https://doi.org/10.1101/631952 may be missing for title: TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity
- https://doi.org/10.3389/fninf.2014.00008 may be missing for title: Dipy, a library for the analysis of diffusion MRI data
- https://doi.org/10.3389/fninf.2019.00064 may be missing for title: The dmipy toolbox: Diffusion mri multi-compartment modeling and microstructure recovery made easy

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 4 years ago

@agahkarakuzu your paper compiled now but it looks like some DOI's are still missing :point_up: can you check/add those?

Kevin-Mattheus-Moerman commented 4 years ago

@agahkarakuzu :wave: how are you getting on? There are some comments to work on above from myself and the reviewers.

agahkarakuzu commented 4 years ago

@Kevin-Mattheus-Moerman I am working on a branch, I will address all the comments this week.

agahkarakuzu commented 4 years ago

[x] Add missing DOIs (@Kevin-Mattheus-Moerman)

Comments by @mfroeling

[x] When the toolbox starts it needs a check if the needed Matlab dependencies are installed. The first few tries I had issues during data processing that were due to missing or badly installed packages. Especially for the missing packages, there should be a strong warning when starting the toolbox that it will not run properly.
[x] Example data is provided for the T1 relaxometry in the documentation. After some browsing the GUI I found the download example button also for other modalities. This should be better documented. I started with the command line and there I could not find a list of available example data.
[x] Each model needs a specific data setup that is apparently inferred from the files in the folder. One can load each data needed separately or by selecting the containing folder. However, for me, it is not clear how the data structure/naming should be for every type of data supported if one wants to used the predefined data format. For example, when additional data quantitative data is loaded how should this be stored (e.g. B1 can be fraction or percent).
[x] I loaded one of my own diffusion sets and the bval/bvec files were not loaded or asked for. without this information the tool still allowed me to click the fit button resulting in errors. Only after some exploration I found the load bval/bvec in the options pannel. Nowhere in the help of the diffusion does it state that I have to load my own bval/bvec files.
[x] different models ask for different input files. This is nicely provided in the GUI however I would be nice if mandatory and optional inputs would be clear. For example, with DTI processing I don't need a mask or SigmaNoise to be able to fit a Tensor.
[x] When I loaded the example diffusion data and then changed the input to one of my own datasets the mask of the previous dataset remained in the Mask input field only after clicking browse and cancel is was cleared. I will open a PR on qMRLab/qMRLab repo (joss_rev2-->master) to respond to the comments in this issue once I check all the items above. Thank you so much, @mfroeling!

openjournals / joss-reviews