Hi Everyone, I'm having a bit of a problem with mri_surfcluster. I ran it alright last week on the right hemisphere, and now am unable to get it to run through with the left. First I'm running mri_glmfit to get .csd files with 10000 iterations (split into 10 runs to speed things up), and then I'm running mri_surfcluster with something like:
mri_surfcluster --in ../SENS/xrun_gavg/lh.osgm.0.5frac.mfx/osgm/sig.mgh --subject average --hemi lh --surf white --annot aparc.a2005s --csd ../csdfiles/mcz_SENS_lh_10000_ mfx_0.5frac_th01_1of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_2of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_3of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_4of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_5of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_6of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_7of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_8of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_9of10-osgm.csd --csd ../csdfiles/mcz_SENS_lh_10000_mfx_0.5frac_th01_10of10-osgm.csd --sum ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/sum_mcz_SENS_lh_10000_m fx_0.5frac_th01 --csdpdf ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/csdpdf_mcz_SENS_lh_10000_m fx_0.5frac_th01 --vwsig ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/vwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --cwsig /clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/cwsig_mcz_SENS_lh_10000_mfx_0.5frac_th01.mgh --o ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/out_mcz_SENS_lh_10000_mfx_0.5frac_th01 --ocn ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/ocn_mcz_SENS_lh_10000_mfx_0.5frac_th01 --olab ./clusters_mcz_SENS_lh_10000_mfx_0.5frac_th01/labels/labels_mcz_SENS_lh_10000_mfx_0.5frac_th01
(in summary: mri_surfcluster --in x --subject average --hemi lh --surf white --annot aparc.a2005s --csd x1 --csd x2 ... --csd x10 --sum x --csdpdf x --vwsig x.mgh --cwsig x.mgh --o x --ocn x --olab x)
When I try to run this I get a segmentation fault. If i take out --csdpdf it will run, but the cluster-wise probabilities in the "sum" file are all the same (-0.1 for one time I tried it, and something like -17 the other time), and the nrep in the sum file is -2 (or -10 the other time I tried) instead of 10000.
Does anyone have any idea what I could be doing wrong? I think everything was recently updated (probably because of the cluster size bug?) because I can no longer re-run last week's right hemisphere analysis using the same csd files (tried this for troubleshooting), so maybe I have to start doing something differently with the new version of this command with the left hemisphere?
Thank you! -Lauren