dtseries generated by HCP functional pipeline

[Asa Borzabadi]

Dear experts,

When working with the functional pipeline, we get to a point where these files are generated:

/SUBID/MNINonLinear/Results/tfMRI_EMOTION_AP/tfMRI_EMOTION_AP_Atlas.dtseries.nii

/SUBID/MNINonLinear/Results/tfMRI_EMOTION_AP/tfMRI_EMOTION_AP_Atlas_s1.dtseries.nii

/SUBID/MNINonLinear/Results/tfMRI_EMOTION_AP/tfMRI_EMOTION_AP_Atlas_hp200_s2.dtseries.nii

- What is the difference between these files? In general, is there any documentation that explains the generated files at each step in detail?

- Are they at fsaverage space? What about the subcortical regions? 

- Are they comparable across subjects? What I mean is that can I use the info of subject 1 and subject 2 and compare the vertices with the same index as being the same in terms of anatomical location? 

Best regards,

Asa Farahani

[Coalson, Timothy Scott (S&T-Student)]

The "hp200" means a high-pass filter was applied.  The _s1 and _s2 sound like smoothing amounts, though I'm not sure exactly what pipeline script makes them (I would guess something in the task pipeline).

We use fs_LR space in the HCP pipelines, not fsaverage.  Specifically, the 91k grayordinates we use for nearly all cifti files (.dtseries.nii is a type of cifti file) are fs_LR 32k for both hemispheres plus voxel-based subcortical structures from MNINonLinear 2mm.

Yes, you can do index-based comparison of 91k grayordinates files across subjects.  The MSMAll versions are better for this if you are interested in functional activation.

Tim

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From: Asa Borzabadi <asa.bo...@gmail.com>
Sent: Wednesday, May 18, 2022 8:22 AM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: [hcp-users] dtseries generated by HCP functional pipeline

 

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[Glasser, Matt]

These sound like intermediate outputs of the task fMRI analysis pipeline.

 

Matt.

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[Asa Borzabadi]

To be clear, I ran the  PreFreeSurferPipelineBatch.sh  ,  FreeSurferPipelineBatch.sh   and  PostFreeSurferPipelineBatch.sh  bash files from the example data and then for functional section, I ran the  GenericfMRIVolumeProcessingPipelineBatch.sh and  GenericfMRISurfaceProcessingPipelineBatch.sh. 

Then I ran the TaskfMRIAnalysis.sh for a subject.

Should I have the MSMAll version at this point?

If so, am I missing a step?

 

I want cleaned MSMAll time courses to work with without going into the FSL task analysis steps, when are these files supposed to be generated? Am I missing running a bash file in this directory (/HCPpipeline-4.3.0/Examples/Scripts) ?

Regards,

Asa Farahani

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[Glasser, Matt]

You should not run TaskfMRIAnalysis until after sICA+FIX and MSMAll.

Matt.

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[Asa Borzabadi]

Thank you! 

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