I'm having an issue running palm following the CIFTI example ( https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/Examples# Example_10:_Using_CIFTI_files). I've worked with PALM a lot, but this is the first time using CIFTI files. I am analyzing several functional tasks from 219 participants in the HCP. I'm running a one-sample t-test with two covariates. The subcortical statistics run fine, but I am having issues with the cortical surfaces.
I was running 10000 permutations and after completing the permutations the job would stall for 10+ hours. When I tried running less (e.g., 500) permutations I get an error from palm_competitive about NaNs. The dpv fwe-corrected stats save (and look reasonable), so the NaN appears during the tfce stage. For the surface I'm using: HCP_S1200_GroupAvg_v1/S1200.R. midthickness_MSMAll.32k_fs_LR.surf.gii along with the mean surface vertex area of the 219 participants. Inspecting the data in wb_view I don't see anything unusual, and no Inf/NaN are indicated in wb_command -file-infomation. Here are the options I am using (I've tried toggling accel, nouncorrected, and logp in different combinations, but the results are always the same): -i lang_story-math_data_L.func.gii -d design_n219_mean.mat -t design_n219_mean.con -o lang_story-math_data_L_cort -T -tfce2D -s L_midthickness.surf.gii L_area.func.gii -logp -n 10000 -ise The relevant files for one example are available here: https://drive.google. com/drive/folders/1uZPQK6Gy2MtTuOjZwin0ZToxBSUN9tct?usp=sharing I've checked everything that I can think of to troubleshoot the issue, but I've hit a wall, so I'd be grateful for any advise/insights. The last thing I'm trying is using the sphere surface, and I'll update if that works. Joe -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A&M Institute for Neuroscience Texas A&M University College Station, TX _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
