Dear experts,
I am trying to use the cluster thresholding command for my freesurfer LME outputs as referred to here https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels. Any feedback or comments would be greatly appreciated.
I am aware that there have been permission denied errors when using mri_surfcluster and that applying this patch ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg should solve the problem (which I tried), however I am still either receiving errors stating the permission is denied.
This is the command I am trying to run:
mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster --sum rh_time_cluster_sum
Here is the error log:
mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster --sum rh_time_cluster_sum thsign = pos, id = 1 version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ hemi = rh srcid = rh_time_spval.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = pos thmin = -1 thmax = -1 fdr = 0.05 minarea = 0 xfmfile = talairach.xfm nth = -1 outid = rh_time_cluster paint sumfile = rh_time_cluster_sum subjectsdir = /gpfs/home/jtl190/work/structurals FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white Done reading source surface Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 1 at vertex 27 overall min = 1.52021e-05 at vertex 125620 surface nvertices 163842 surface area 65020.929688 surface area 65020.765625 Setting voxel-wise threshold with FDR = 0.050000 Assuming input map is -log10(p) MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=1.04576 FDR Voxel-wise threshold is 1.04576 Adjusting threshold for 1-tailed test. If the input is not a -log10(p) volume, re-run with --no-adjust. Searching for Clusters ... thmin=1.045757 (0.744727), thmax=-1.000000 (-1), thsignid=1, minarea=0.000000 Found 9803 clusters Max cluster size 5993.586426 INFO: fixing MNI talairach coordinates Saving thresholded output to rh_time_cluster Can't create file /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w
Permission denied
Thank you for taking the time to read this email.
Sincerely,
Jennifer Legault