Horos (Osirix) BIDS Output extension

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Michał Szczepanik

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Jan 10, 2018, 2:11:13 PM1/10/18
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Dear (Brain Imaging Data) Structured People

Recently, I returned to my project from the CRN Coding Sprint in August, a Horos / Osirix Bids Output Extension. The aim of the plugin is to help in conversion from raw DICOMs to a BIDS dataset. I think it now has enough functionality to be shared with the mailing list. 

The project (and the compiled plugin) can be found on GitHub: https://github.com/mslw/osirix-bids-output. For more details see the GitHub page and the rest of this e-mail below.

What and Why:
Horos and Osirix are DICOM image browsers for MacOS, with a reasonably capable database system. Side note - Osirix and Horos are identical to a large extent, as Horos forked from Osirix at some point; since August, our lab switched to using Horos, hence I put both names in the title. In our lab, MR images are sent from the scanner to a PACS server and we normally use a computer running Horos to query the server and export somewhat sorted DICOMs for further processing.

Although BIDS converters, such as heudiconv, already exist, the idea behind this plugin was to create a GUI tool, which would allow users to enter a mapping from sequence names to BIDS terms and output a basic BIDS structure of NifTI files, all from within Horos (without requiring a specific scheme on scanner console level, config files or command line tools).

The plugin gets user input, sorts DICOMs accordingly and utilises dcm2niix (called as an external process, to be installed separately) to perform conversion. It has some logic for handling repeating series names and discarding series that are too short. There are some limitations to what it can do, some of which I will most likely work on and some of which that will have to be left to other tools. Some of them include handling field maps (so far there is logic only for the case of 1 phasediff and 2 magnitude images), name validation (none performed - this is left to the user), number of fields and suffixes available (I’m planning to add them, but the most common are there) and handling json sidecars (dcm2niix output is left untouched). Considering all of this, I think the time is right to call it a 0.1 version release and publish the binary on GitHub.

In the coming days, we will be trying it out in our lab. I realize that our setup (using Horos to query PACS) may not be a very popular way of fetching data from the scanner, but if there are Horos users on the list (or somebody is curious to check it out), I will be very happy to read your comments.

With this, I would also like to say thank you to Chris Gorgolewski, Tal Yarkoni, Satrajit Ghosh and Cameron Craddock for their valuable brainhack comments.

Yours Truly
---
Michał Szczepanik, Ph.D. candidate
Laboratory of Brain Imaging (LOBI)
Neurobiology Center
The Nencki Institute of Experimental Biology
Pasteur 3, 02-093 Warsaw, Poland
Tel.: +48 22 5892 550
website: http://lobi.nencki.gov.pl/


Dan Lurie

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Jan 10, 2018, 4:20:17 PM1/10/18
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This is great, Michal! I know there are a bunch of people in my group who want to use BIDS but are a bit intimidated by heudiconv. I’ll pass this along to them and report back if we end up trying it.

Dan Lurie
@danjlurie
http://danlurie.org
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Chris Gorgolewski

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Jan 10, 2018, 5:55:11 PM1/10/18
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Fantastic development Michał!

Best,
Chris

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Tal Yarkoni

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Jan 10, 2018, 7:10:03 PM1/10/18
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Thirded--wonderful contribution!

Michał Szczepanik

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Jan 15, 2018, 8:30:25 AM1/15/18
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Thank you for your kind words!

Dan - If your group does end up trying it, I’ll be very happy to hear your impressions. I haven’t tested many cases and I guess there are some improvements I should be able to add without much hassle. Please keep in mind that the plugin is mostly concerned with organizing NifTIs and providing leaving .json sidecars as they come from dcm2niix, so the additional info (some JSON fields, events.tsv etc) will have to be generated by the user anyway.

Best
Michał Szczepanik

Wiadomość napisana przez Tal Yarkoni <tyar...@gmail.com> w dniu 11.01.2018, o godz. 01:09:

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Catherine Morgan

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Mar 18, 2018, 8:03:26 PM3/18/18
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This sounds great, will take a look at the GUI, thanks Michal.

 

If there are people not doing the conversion through a GUI and Horos, but as Dan mentioned, a bit intimidated by heudiconv I wrote up some instructions for researchers at our centre in Auckland

 

https://github.com/Neuroimaging-RG/BIDS_conversion/wiki

 

thanks

 

Catherine

Michał Szczepanik



 

Thirded--wonderful contribution!

 

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Chris Gorgolewski

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Mar 18, 2018, 9:10:23 PM3/18/18
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This looks great! Thanks for sharing!

I wonder if it would make sense to add this link to BIDS Starter Kit - https://github.com/INCF/bids-starter-kit/wiki/BIDS-Wiki and/or heudiconv documentation.

Best,
Chris

Michał Szczepanik



 

Thirded--wonderful contribution!

 

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