B1+ bias correction update?

[Victoria King]

Hi HCP experts,

I've been keeping track of the suggestions to use transmit field bias correction of the T1w/T2w myelin maps. I was wondering if the code is published yet, or if there is an estimate of when that code will become available?

Thank you so much,

Victoria

[Tim Coalson]

No, it is not published yet, sorry.  Estimates are difficult, but probably this year.

Tim

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[Victoria King]

Thanks for the update!

Victoria

[Erica Howard]

Hello! I just wanted to confirm that this B1+ correction (allowing for cross-group analysis) was not included in the recent 4.8.0 release right?

Thanks for your help!

Erica

[Glasser, Matthew]

There is a pull request that has this now, if you want to try it.  Given that this is not yet accepted code, we don’t guarantee that it won’t change before a release.  We do intend for the next official release to have this feature and apologize for the long delay in getting it available.

Matt.

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[Erica Howard]

Not a problem, I'll check out the pull request. Thanks for the update!

[Victoria King]

Hi all,

Following up on the pull request that is currently available - could you walk me through how to use the code? I'm not very familiar with using Github. What is the order in which I should use the scripts? How does the transmit bias correction script fit into the original PreFreeSurfer, FreeSurfer, and PostFreeSurfer pipelines?

Thank you all so much, and I'm looking forward to using the finalized scripts with the next version. Just wanting to get a feel for them now.

Victoria

On Thursday, September 19, 2024 at 2:13:55 PM UTC-4 glas...@wustl.edu wrote:

[Glasser, Matthew]

Transmit field correction of T1w/T2w myelin maps would typically be run after MSMAll in humans, though after MSMSulc is okay in monkeys.

Matt.

[Victoria King]

Dr. Glasser,

Thanks for the quick reply. I am looking to apply the transmit field correction to structural images in humans. All of my subjects have been processed through PreFreeSurfer, FreeSurfer, and PostFreeSurfer. Do I run the transmit field correction step after that? I'm assuming I would run the Phase 1 - Phase 4 pipelines found here in order?

Thanks, 

Victoria

[Glasser, Matthew]

Do you not have fMRI data?  If I recall correctly, this pipeline benefits from having an MSMAll multi-modal alignment so that the myelinated hotspots line up.

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[Victoria King]

Oh, I see now. So, to confirm, the order of the pipelines including the transmit bias step should be run as follows:

PreFreeSurfer -> FreeSurfer -> PostFreeSurfer -> Generic fMRI Volume Preprocessing -> Generic fMRI Surface Preprocessing -> ICA Fix Pipeline -> MSMAll -> Phase1_IndividualAlign -> Phase2_GroupAverageFit -> Phase3_IndividualAdjustment -> Phase4_GroupAverageCorrectedMaps

At that point, I can run wb_command -cifti-parcellate on the output files from the Phase 4 pipeline to extract transmit field bias-corrected myelin values for each ROI within a given atlas.

Does this sound correct to you?

Thanks,

Victoria

[Glasser, Matthew]

I would also run DeDriftAndResample after MSMAll. 

 

Yes, you could do that.  We will need to get the official IDP pipelines committed at some point, but that is one of the things the structural pipeline does.

Matt.

[Tim Coalson]

The Examples/Scripts/TransmitBiasBatch.sh script is intended to make it easy to run the four phases of transmit bias on a cluster.  You should still do MSMAll first, obviously.

Tim

[Victoria King]

Great. Thank you both so much for your help.

Victoria