Running FreeSurfer v7.2 on unprocessed HCP T1s

[Carly McIntyre-Wood]

Hi there,

 

I tried to submit this question another way, but I’m not sure I was successful. My apologies if this ends up being a duplicate!

 

My lab has processed HCP raw T1s using Freesurfer v7.3 and hippocampal/amygdala segmentation without error; however, when reading Glasser at al., 2013, it seems as though the use of unprocessed data is not advised. Do you think this volumteric data will be inaccurate? If so, do I need to repeat the process using some sort of output from the PreFreeSurfer processing?

 

Thank you so much for your time.

Carly

 

 

[Glasser, Matt]

That depends on what your goals are.  If you want to use subsequent HCP Pipelines you should run things through FreeSurfer 6 and PreFreeSurfer.

Matt.

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[Carly Wood]

Hi Matt, 

Thanks so much for for getting back to me! We do not wish to use subsequent HCP pipelines, we just wish to continue analysis using the hippocampal and amygdala volumes we have generated. My fear is that they may not be accurate without the PreFreesurfer step. It was the below sentences that have me worried:

" Many of the HCP datasets are qualitatively different from standard neuroimaging data, having higher spatial and temporal resolutions and differing distortions. As a result, these data must be processed differently to achieve optimal results. Users of unprocessed data must deal with complex and esoteric issues that are particularly relevant for these acquisitions, such as the correction of gradient nonlinearity distortion in images that were acquired with oblique slices relative to the scanner’s coordinate system."

Carly

[Glasser, Matt]

Which data are these?

Matt.