Hello, I had emailed the Freesurfer Forum a few weeks back about trying the PALM analysis for permutation testing. I recently tried fsPalm again on running some of our subcortical analyses for the caudate, putamen, and nucleus accumbens, and we performed the following steps:
* Set our respective ROIs (e.g. caudate, putamen, nucleus accumbens) * Set the paths for fsPalm to run for each of the ROIs * Ran mri_glmfit as noted in the Freesurfer Help documentation for fsPalm for the three ROIs We ran into several issues. When we looked in the ‘run_palm.m’ output file under the subfolder for our first ROI that we tried to run PALM analysis for, it mentions ‘error in run_palm: zthresh = fast_p2z(pthresh)'. We are not sure where this function fast_p2z is supposed to be called from, as it is not located in any of the Matlab scripts when downloading the package for fsPalm (e.g. the palm-alpha115 file from Freesurfer). My question is - are we missing a path, or several paths that we have to put into the Matlab script, or does fsPalm no longer work for running such analyses? fsPalm has worked in the past for one of my colleagues using the palm-alpha112 file, but we are now having trouble running this using the palm-alpha115 file version. Any help would be greatly appreciated. Thanks, Amritha Amritha Harikumar Clinical Research Coordinator Holt Emotion and Social Neuroscience Lab Department of Psychiatric Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital ___________________________ 149 13th Street, Rm 2620A Charlestown, MA 02129 Phone: 617-724-3283
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