It depends on what you eventually want to do with it. The warning was so that people would not go off and do, eg, correction for multiple comparisons or something where there was some assumption about consistency between the surface-based and volume-based results.

On 2/22/19 3:18 PM, Haroon Popal wrote:

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Hello FreeSurfer Developers,

I have functional contrast maps from the HCP dataset. I converted these to fsaverage space and now have GIFTIs for the surface data and a NIFTI for the subcortical volume data. I would like to combine these into one file for an analysis where I will be predicting the intensity of individual voxels. I thought I would use vlrmerge to do this, but noticed that the documentation notes that vlrmerge should only be used for visualization purposes. I was wondering if you thought that doing my analysis on the vlrmerge output would be a bad idea, even though I am not doing any real computation on the merged volume maps.

If this is a bad idea, is there another method that I can use to combine the surface and subcortical volume data?

Thank you.

-- Haroon S. Popal Ph.D. Student Cognitive Neuroscience Laboratory Department of Psychology | Temple University

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