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gbook / nidb

NeuroInformatics Database
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Beginner questions #55

Closed dorianps closed 6 years ago

dorianps commented 6 years ago

Hi, I was advised NIDB by one of my colleagues and I find it to be impressive from the tutorials. Congrats.

I have several questions though, some of which are below while others may come later.

  1. Where can I find the complete documentation? Currently, Sourceforge seem to be down, maybe there is documentation elsewhere.

  2. Why is FSL needed as requirement? Can NIDB work without FSL and with other software instead, like ANTs/Freesurfer? Asking because FSL is not entirely open source, and require special licenses for commercial use.

  3. I have already data in BIDS format. Is there any cross compatibility with BIDS data?

  4. I am trying to understand differences of NIDB with other management solutions, like datalad.org or XNAT. I.e., one of the features of Datalad is versioning of big files, so if any file is changed in the storage - even by mistake - there is a tracking system that enhances reproducibility efforts. How is something like this, for example, handled in NIDB.

Thank you. Dorian

gbook commented 6 years ago

Hi Dorian, Thanks for the message. The most complete documentation for usage will be on the github repository in the documentation directory. Anderson Winkler has a good tutorial on how to install it on brainder.org. FSL is used to calculate motion correction and other QA metrics on MRI data. I have not tested it without FSL, but I imagine some parts will work, and some will not. We do not yet have any support for BIDS format, as the DICOM and par/rec formats have taken care of our needs for sharing data. If there is significant interest in adding BIDS support, then we can work on that.

NiDB is similar to other databases in that it stores imaging data and the associated demographics. It's different because it stores any type of data, including assessments, QC, and any other type of binary data, in a consistent hierarchy. The pipeline system is built off of the data storage system. There is no versioning with the raw data storage, as it's expected that the raw data is original and unchanged. The pipelines have versioning with the scripts themselves, but not the processed data. If you perform an analysis on a dataset, you can view which version of the pipeline script was run. There are tools for grouping data.

Hopefully this answers your questions! -Greg

dorianps commented 6 years ago

Thanks for the detailed response @gbook . Will give it a try these days and come back if more questions come up. As to BIDS file structure, there are many labs and software tools that rely on those, so it would definitely help the integration of NIDB with existing work. But I understand this might not be straightforward to change. The NiDB strength is the gui, which seems great.

Thanks again.

gbook commented 6 years ago

Just curious, what software/labs use BIDS?

dorianps commented 6 years ago

E.g., Center for Brian Imaging at Dartmouth, but also some labs at U. of Iowa. We also have converted most of the dicoms in BIDS format. There is a number of BIDS dockers which can be used off the shelf to run analyses easily (https://github.com/BIDS-Apps), and looks like there is a possibility to run analyses online if the data and the software follow the BIDS format (http://openneuro.org/) . There is some more info at http://bids-apps.neuroimaging.io/apps

Hope it helps.

andersonwinkler commented 6 years ago

All new projects we are starting (4 presently) are using BIDS format. It feels lots of people are moving to it too, to facilitate data sharing and reuse of code...

On Wed, 27 Jun 2018 at 17:06, dorianps notifications@github.com wrote:

E.g., Center for Brian Imaging at Dartmouth, but also some labs at U. of Iowa. We also have converted most of the dicoms in BIDS format. There is a number of BIDS dockers which can be used off the shelf to run analyses easily (https://github.com/BIDS-Apps), and looks like there is a possibility to run analyses online if the data and the software follow the BIDS format (http://openneuro.org/) . There is some more info at http://bids-apps.neuroimaging.io/apps

Hope it helps.

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dorianps commented 6 years ago

@andersonwinkler

How are you integrating BIDS and NiDB?

P.s. I was just about to write you to follow up on our brief chat.

andersonwinkler commented 6 years ago

I'd happily work with Greg to make this available for NiDB users. It'd be great if BIDS could be an option when downloading.

On Wed, 27 Jun 2018 at 17:19, dorianps notifications@github.com wrote:

@andersonwinkler https://github.com/andersonwinkler

How are you integrating BIDS and NiDB?

P.s. I was just about to write you to follow up on our brief chat.

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