Is there DWI data aligned to MNI space in HCP database?

[Pavithra Rajeswaran]

Hello everyone,

I’m Pavi, a PhD student at the University of Washington Seattle. I’m working on a class project and I’m really excited about using the HCP dataset to study the connections between the structure and function of the brain. This is my first time analyzing this dataset, so I’m a bit new to it. I was wondering if there’s any DWI image data that’s already aligned to MNI space that I could use? 

I was able to access the database and download fMRI and DWI data for a subject 100307 from the paths below. Please let me know if there are the ones I should look at. 

fmri: HCP_1200/{subject_id}/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz  

DWI :HCP_1200/{subject_id}/T1w/Diffusion/data.nii.gz 

(this is aligned to T1 space?)

Please let me know if there are any tutorials that I can see related to this. Thank you!! 

Best,

Pavi 

[Tim Coalson]

Tractography makes the most sense in the original shape of the individual's brain, so we only resample the diffusion data to the T1w (rigid rotation) space and correct for distortions.  The volumetric fMRI is in MNINonLinear space because that is how we put the subcortical data into CIFTI space, and we don't want to generate two versions of the volume timeseries for storage space reasons.

The cifti form of the fMRI is more useful for comparing across subjects than the volume form.  We also recomment that diffusion tractography be tracked to the cortical surface, rather than a voxel-based mask, partly because the corners of voxels stick out more when the track is diagonal than when it is close to axis-aligned.  We also haven't validated a particular tractography method, the ones we have tried tend to suffer "gyral bias", where the streamlines don't fan back out in a white matter blade, resulting in far lower total hit density on sulcal banks than on gyral crowns, which implies inaccuracy of the track endpoints.

Tim

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[Glasser, Matthew]

You can use ${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz to resample the diffusion data or DTI parameter maps to MNI space.

Matt.

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