Question about HCP pipeline version

[杨国元]

Hi HCP experts，

We use the HCP-YA S1200 Caucasian data and our Chinese HCP data to perform the comparison study in brain parcellation.Specifically, the preprocessing step of CHCP uses the HCP pipelinev4.0.0, but the preprocessed data of HCP were download from ConnectomeDB (S1200), which using HCP pipelinev3.4.0 or other version. The detailed CHCP data preprocessing steps using v4.0.0 are mainly include structural MRI (prefreesurfer, freesurfer, postfreesurfer), functional MRI (fMRIVolume, fMRISurface, ICA-FIX), diffusion MRI (diffusionPreprocessing) preprocessing. But we are not sure what is the main difference between these two versions (v3.4.0 and v4.0.0) of HCP pipeline? Will it have a large impact on the results of data analysis? 

Best regards,

Guoyuan

Guoyuan Yang

Center for MRI Research

School of Physics

Peking University

Beijing, China

Tel：18800172884

Email：yangg...@pku.edu.cn

[Glasser, Matt]

Some changes worth considering (versus the latest version in the GitRepo):

 

1. The fMRI bias field correction was fixed (it was also fixed after processing in Glasser et al., 2016 Nature).  We hope to fix this in the future together with some denoising improvements.
2. The MSM algorithm has been improved, resulting in slightly better alignment and less distortion.
3. We now use MR+FIX (though you need to make sure to use the correct training file).  Also the task fMRI data have not been denoised. 
4. We now use many more flags in eddy like slice-to-volume registration and susceptibility by motion interaction.
5. We use FreeSurfer 6.0 instead of 5.3-HCP, which have similar performance. 
6. There are some new QC outputs for structural and fMRI data. 

 

These are the most important changes that I can think of off-hand.  If you use effect size maps with fMRI, you do need the bias correction fixed (though z-stat maps have a different inherent normalization).  Effect size maps are more biologically meaningful. 

Matt.

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