Hi, I have run qdec for a simple contrast comparing thickness across the cortical surface between a patient and control group. Not much survives vertex-wise FDR correction, and I would like to try cluster- based thresholding. I would like to make sure I understand the inputs to the command. Am I correct on the following?
--in = the signifcance values (i.e., contrast_name.sig.mgh file) --thmin = the vertexwise threshold for determining clusters, where 2 corresponds to p=.01 --minarea = the cluster extent threshold - Am I correct in assuming this should not be smaller than the smoothing kernel?
When I run the command below, I get the following output. Only one (whole hemi) cluster is identified. I'm not sure if its a problem in my command line, or with my data. Also, I seem to have the --cwsig flag wrong, but can't figure out the error (appending .w or .label to the end of the output filename does not change the error).
I greatly appreciate your help.
mri_surfcluster --in qdec/MF_group_lh/contrasts.sig.mgh --subject fsaverage --hemi lh --surf white --annot aparc --sign abs --thmin 2 -- minarea 25 --sum stats/qdec_run/cluster/summary.txt --o stats/ qdec_run/cluster/cluster_output --cwsig stats/qdec_run/cluster/cwsig --olab stats/qdec_run/cluster/MF_group_lh_thk
thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = lh srcid = qdec/MF_group_lh/contrasts.sig.mgh paint srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr = -1 minarea = 25 xfmfile = talairach.xfm nth = -1 outid = stats/qdec_run/cluster/cluster_output paint sumfile = stats/run2/cluster/summary.txt subjectsdir = /data/kang/work/struct/alex/freesurfer/subjects_cann FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /data/kang/work/struct/alex/freesurfer/subjects_cann/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 /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/lh.white.avg.area.mgh Done reading source surface Reading annotation /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/ buckner_cortical_atlas/scripts/colortable_final.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 43.1907 at vertex 101931 overall min = 7.66111 at vertex 28089 surface nvertices 163842 surface area 65416.985991 surface area 65416.985976 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, minarea=25.000000 Found 1 clusters Max cluster size 103339.460938 INFO: fixing MNI talairach coordinates Saving thresholded output to stats/qdec_run/cluster/cluster_output avg = 35.029, stdev = 4.669, min = 7.661, max = 43.191 Saving cluster pval stats/qdec_run/cluster/cwsig unknown file type for file (stats/qdec_run/cluster/cwsig) LabelWrite: saving to stats/qdec_run/cluster/MF_group_lh_thk-0001.label
Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne
Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia
Ph: +61 3 8344 1861 Fax: +61 3 9348 0469
fornitoa@unimelb.edu.au