Applying the CBIG preprocessing pipelines to the HBCD dataset?

[Alexander Cohen]

Hi all,

Has anyone been able to run HBCD data through the CBIG pipelines?

We have been trying to, but the provided free surfer files are missing a required file: talairach.m3z, which is typically generated during recon-all and located in mri/transforms/talairach.m3z and seems to be required for the CBIG preprocessing pipeline.

I understand that the infant brain does not align perfectly with the standard adult Talairach space. However, is it possible to generate this file so that we can use our current processing pipeline (to be consistent across datasets?).

(We've been trying to do get this to work for months now... running recon-all ourselves is leading to really poor registrations...)

I asked Damien Fair about the HBCD processing and this was his reply:

"We use Nibabies/fMRIprep Lifespan for this. The file you want may not exist depending on the age. There is a two step process to get the data into MNI, not talairach, and then the surface generation is done (MCRIBS) for the younger kids. Are you using the adult recon-all on the infant brains? That typically won't work."

Any ideas from this group?

-Alex Cohen

[Thomas Yeo]

Hi Alex, we have not tried running our pipeline on HBCD. We typically use ants nowadays instead of m3z to project to mni space. Have you tried to see if that works for infants? 

Regards,

Thomas 

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[Alexander Cohen]

Hi Thomas, I’ll work with my staff and see if we can bypass things with ants

-Alex

 

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Dr. Alexander Li Cohen, MD, PhD, FCNS, FAAN

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From: Thomas Yeo <yeoy...@gmail.com>
Sent: Saturday, May 9, 2026 6:29:32 PM
To: Alexander Cohen <alex...@gmail.com>
Cc: CBIG users <cbig_...@googlegroups.com>
Subject: Re: [cbig_users] Applying the CBIG preprocessing pipelines to the HBCD dataset?