Update dcm2niix within an existing dcm2bids environment

[ilaria]

Summary of what happened:

Hello!

sorry for the many questions, any help is appreciated!

The scanner was updated to AX30 and the file format apparently requires the newest version of dcm2niix.
Previously, I was successfully using dcm2bids and would like to continue using it.
a) is this still possible if I update the dcm2niix?
b) are there instructions/tutorials on how to only update the dcm2niix when the environemnt is with Docker? If not, do I need to reinstall/recreate the environment?

The next question is about the new file output received from the scanner.
The old folders, after unzipping them, were as follows:

* - StudyName_Sub#_PIName_date_numbers
*            - MOCOSERIES_001
*            - MPRAGE_002
*            - TASK_003
*                 - study name_PIname_ long string of numbers

New folders are:

>  -StudyName_Sub#_date
>         - study name_PIname_ long string of numbers

With the new system, I don’t have the subfolders telling me which acquisition each files belongs to. How can I fill out the dcm2bids configuration files in this case? I’m also waiting to hear back from the scanner tech to make sure it wasn’t an error when sending me the files.

Once I successfully export the new files to NIFTI, do I need to make changes to fMRIprep and AFNI for processing?
Because part of my participants were acquired before the update, are there specific considerations I need to keep in mind if I want to group them for analyses?

Thank you,
Ilaria

[Steven]

Hi @ilaria,

@ilaria

a) is this still possible if I update the dcm2niix?

Yes

@ilaria

b) are there instructions/tutorials on how to only update the dcm2niix when the environemnt is with Docker? If not, do I need to reinstall/recreate the environment?

You can either (1) ask the developers to release a new container with the latest dcm2niix (@abore) . (2) Bind a local version of dcm2niix into the Docker container when you run it (probably the more complicated, least recommended method). (3) Use dcm2bids in an Anaconda virtual environment, where you can control software versions.

@ilaria

With the new system, I don’t have the subfolders telling me which acquisition each files belongs to. How can I fill out the dcm2bids configuration files in this case?

After running dcm2bids_helper you can look at the JSON files and see what can be used to associate with each scan. Usually SeriesDescription is a good bet.

@ilaria

Once I successfully export the new files to NIFTI, do I need to make changes to fMRIprep and AFNI for processing?

No, as long as the file structure is BIDS valid, fMRIprep should run fine.

@ilaria

Because part of my participants were acquired before the update, are there specific considerations I need to keep in mind if I want to group them for analyses?

Unsure, maybe @neurolabusc would know better?

Best,
Steven