arrange data / BIDS

[oumayma soula]

hello all; 

after transforming my data to NIFTI format i get this ( T1 and fMRI  in same folders):

How can I arrange this data to conform to the BIDS format? Note that the numbers mentioned are related to the visits. I also have a CSV file to match the dates and visits (sessions), which might be helpful! Could you please provide the steps to do this? I want to follow this directory structure:

thank u !

[Arnaud Boré]

Hi Ouma,

You can use Dcm2bids and skip the dcm2niix part using this option--skip_dcm2niix
Check the documentation: https://unfmontreal.github.io/Dcm2Bids/3.2.0/

If you have any questions don't hesitate to post it on https://neurostars.org/ there are plenty of users who have similar issues and can help you.

Best,

Arnaud

[oumayma soula]

Well received with thanks.

--

Oumayma SOULA

PhD candidate in Computational Neuroscience

Faculty of Medicine of Sfax, Tunisia

Phone number: +216 26 137 126.

LinkedIN: linkedin.com/in/oumaïma-soula

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[Marcel Zwiers]

I think dcm2bids, heudiconv and bidscoin (not in any order) are probably the 3 most popular bids converters out there (but there are many more). Each has its pros and cons, so check them out to see which one suits you best.

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[Dianne Patterson]

Let me add ezbids, which is online through Brainlife.  My students adore ezbids: https://brainlife.io/ezbids/

-Dianne

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Dianne Patterson

dian...@gmail.com 

[oumayma soula]

Thank you for the recommendation. I like it; it is user-friendly. I have started using it, but I'm getting an error when I use data from two patients. How can I solve this?

[Dianne Patterson]

Hmm, you might need to ask the developer.  Let him know what scanner the data is from.

-D

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Dianne Patterson

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[oumayma soula]

Okay 

I will do 

Thanks a lot !

--

Oumayma SOULA

PhD candidate in Computational Neuroscience

Faculty of Medicine of Sfax, Tunisia

Phone number: +216 26 137 126.

LinkedIN: linkedin.com/in/oumaïma-soula

To view this discussion on the web visit https://groups.google.com/d/msgid/bids-discussion/CAGpV9F%2B3LV70JoddTM-XiUvQ9_JHgD1K%2BjXiPLh%2BXBi92_2UAA%40mail.gmail.com.

[Anthony Galassi]

Hi Oumayma,

You should reach out to ezBIDS either through their brainlife.io slack or post an issue here on github with the same screenshot from earlier. In the meantime you should collect individual logs from that page to help in debugging, with logs and the "session" id contained in the URL the ezBIDS team should be able to diagnose what sort of issue it is your encountering. 

Could be something as simple as a connection issue or a private tag in a dicom causing some headache.

Thanks,

Anthony

[oumayma soula]

Ho @Anthony

 Those guidelines were so helpful, thank you a lot. I solved the problem. 

 However, I am facing an issue joining Brainlife's Slack.  

[Anthony Galassi]

Hi Oumayma,

Hmm, I'm not able to do too terribly much to help on that end, but I'm going to point the brainlife slack admin's to this discussion. In the meantime I'd suggest emailing them at in...@brainlife.io as they're very responsive.

Alternatively, one can run ezbids locally if they so chose, that I could help you with if you're able to install docker and docker compose on you own hardware.

Thanks,

Anthony

[oumayma soula]

Hi Anthony

Oh, thanks a lot. I really appreciate it

Okay i will install too.

 thanks ,

[oumayma soula]

Hi anthony

please  I have another question. If I choose to use Brainlife resources, how much does this affect the privacy of my data? My data is private, and I have no right to share it.

 thank you !

[Anthony Galassi]

Hi Oumayma,

I can't speak to that as I'm not aware of how/where data gets stored after it leaves ezBIDS.

Oh and to get back to you, if you just want to run the conversions locally you can do so by starting ezBIDS with the dev.sh script and the -d argument, see below:

Thanks,

Anthony

[oumayma soula]

Hi

Thanks alot Anthony

I downloaded Docker and set it up for use with Brainlife/cli. I'm still experimenting with it to discover more 

--

Oumayma SOULA

PhD candidate in Computational Neuroscience

Faculty of Medicine of Sfax, Tunisia

Phone number: +216 26 137 126.

LinkedIN: linkedin.com/in/oumaïma-soula

To view this discussion on the web visit https://groups.google.com/d/msgid/bids-discussion/cbfe8be4-4725-4f87-b7bc-11076d689955n%40googlegroups.com.