Hi Chris et al.,

I've recently used PALM with various 4D .mgh input files (i.e., subjects' mri_concat[enated] lh.thickness.fwhm15.fsaverage.mgh files, for example), so PALM's results are in .mgz format. I can convert these to .nii using mri_convert in order to use fslmaths/fslstats and load them into Surf Ice, but the overlay is a uniform map with (what appears to be) 0 at all vertices. In case it's relevant and you're familiar with PALM, I've generally used the -logp option in order to save resulting p-values on a -log10p scale, as suggested by Anderson Winkler, but perhaps this complicates things for Surf Ice. I've run into various quirks loading results in Freeview, which has partially led me to explore Surf Ice, but the maps are generally interpretable and highly significant as viewed in Freeview. For example, there should be three significant clusters in the attached screenshot of one .nii overlay (inferior precentral, superior parietal, and inferior parietal).


Do you have any suggestions on how I might go about either 1) properly loading these results in Surf Ice or 2) modify the PALM input or output files so that Surf Ice can correctly display these results?

Many thanks for your help, and thank you for creating such a beautiful, user-friendly rendering tool for the neuroscience community! It's truly beautiful :-)


With gratitude,
Dan