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Dear Freesurfer Developers, I'm using PALM to run permutation analyses to correct for multiple comparisons on Freesurfer cortical thickness and LGI data. fspalm from a command like "mri_glmfit-sim --glmdir lh.lgi.glmdir --perm 1000 2 pos --cwp .05 --2spaces" produces output files including *.cluster.mgh - map of signifcant clusters, *.cluster.summary - text file of of cluster table (incl. sizes, cluster annotation, MNI coordinates, and significance), and *.y.ocn.dat – text file containing LGI or cortical thickness values for each subject from significant clusters. I was wondering if PALM produces similar output? From my understanding the *clustere_tstat_fwep.mgz file from PALM would be equivalent to the *.cluster.mgh from fspalm, but is there any way to get a text file of the cluster table or of the LGI/CT values for each subject from significant clusters?I would like to report significant clusters (ie. coordinates or parcellation, cluster size, pvalue) in a table and also to extract the average lgi/thickness from significant clusters for each subject.
Thanks very much Colleen