Thanks for your help Pratap. I've actually been trying to follow the tutorial and was running simulations initially, but when I tried to re-trace my steps I ended omitted them because I forgot they were necessary for mri_surfcluster.
Either way, the results are the same- I still get one whole surface cluster as output even after running simulations. In this case, I re- ran it copying your commands, except I used perm because I have low numbers and no covariates. I also ran 1000 permutations, to get a quick initial result for testing. My commands and output are below.
I would appreciate further help on this, as I'm not sure where I'm going wrong!
also, I noticed that after your mri_glmfit command, you added --i divided into 5000 each. Sorry, but I'm not sure what you meant by that.
mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd qdec/MF_group_rh/ qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C qdec/ MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm 1000 2 stats/ newperm_rh/newperm_rh --glmdir stats/newperm_rh/
gdfReadHeader: reading qdec/MF_group_rh/qdec.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 group1 2 group2 INFO: gd2mtx_method is doss Reading source surface /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/rh.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/rh.white.avg.area.mgh simbase stats/newperm_rh/newperm_rh Number of vertices 163842 Number of faces 327680 Total area 65020.765625 AvgVtxArea 0.396850 AvgVtxDist 0.717994 StdVtxDist 0.193566 reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/rh.white.avg.area.mgh INFO: fwhm2niters: Fixing group surface area Surface smoothing by fwhm=34.309616, niters=866.000000
$Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /data/kang/work/struct/alex/freesurfer/subjects_cann cmdline mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd qdec/MF_group_rh/ qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C qdec/ MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm 1000 2 stats/ newperm_rh/newperm_rh --glmdir stats/newperm_rh/ sysname Linux hostname kang machine i686 user alex FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 34.309616 niters 866.000000 OneSampleGroupMean 0 y /data/kang/work/struct/alex/freesurfer/subjects_cann/qdec/ MF_group_rh/y.mgh logyflag 0 usedti 0 FSGD qdec/MF_group_rh/qdec.fsgd glmdir stats/newperm_rh/ DoFFx 0 Loading y from /data/kang/work/struct/alex/freesurfer/subjects_cann/ qdec/MF_group_rh/y.mgh Matrix condition is 1 search space = 82167.6 Smoothing input by fwhm 34.309616 Smoothing done, nsteps = 866, tsec = 1236.17 ... done DOF = 28 thresh = 2, threshadj = 2 Starting simulation sim over 1000 trials 1/1000 t=0 ------------------------------------------------ Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Diff-1-2-Intercept 0 nc=3 maxcsize=1910.81 sigmax=-3.00831 Fmax=13.551 2/1000 t=0.0572833 ------------------------------------------------ Starting fit and test 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Diff-1-2-Intercept 1 nc=0 maxcsize=0 sigmax=1.36036 Fmax=4.46612 3/1000 t=0.0994333 ------------------------------------------------
... and so on... then
mri_surfcluster --src qdec/MF_group_lh/contrasts.sig.mgh --csd stats/ newperm_lh/newperm_lh-Diff-1-2-Intercept.csd --sum stats/newperm_lh/ newperm_lh --ocp stats/newperm_lh/newperm_lh.mgh
thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = rh srcid = qdec/MF_group_lh/contrasts.sig.mgh paint srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr = -1 minarea = 0 xfmfile = talairach.xfm nth = -1 sumfile = stats/newperm_lh/newperm_lh 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/rh.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/rh.white.avg.area.mgh 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 = 43.1907 at vertex 101931 overall min = 7.66111 at vertex 28089 surface nvertices 163842 surface area 65020.838384 surface area 65020.838382 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, minarea=0.000000 Found 1 clusters Max cluster size 103836.125000 INFO: fixing MNI talairach coordinates Saving cluster pval stats/newperm_lh/newperm_lh.mgh
On 04/12/2007, at 11:30 AM, Pratap Kunwar wrote:
Alex,
You have to do simulations using mri_glmfit before youdo mri_surfcluster,
[more info in this link at https://surfer.nmr.mgh.harvard.edu/fswiki/ FsTutorial_2fGroupAnalysis?action=highlight&value=fsgd go down to [4.0 Using mri_glmfit to correct for multiple comparisons: ]
USAGE: ./mri_glmfit
--glmdir dir : save outputs to dir
--y inputfile **y.mgh --fsgd FSGDF <gd2mtx> : freesurfer descriptor file **qdec.fsgd --C contrast1.mat <--C contrast2.mat ...> --fwhm fwhm : smooth input by fwhm ** your smoothing value from " fwhm.dat" --surf subject hemi <surfname> : needed for some flags (uses white by default) **lh or rh --sim nulltype nsim thresh csdbasename : simulation perm, mc- full, mc-z **mc-z (i used) is faster than mc-full, minimum threshold value ( i.e. 1.3 for 0.05),
My command was more like this,
mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf fsaverage rh -- fwhm < ??
--C contrast/contrastname.mat --sim mc-z 5000 1.3 f11/csd1 -- glmdir f11
mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf fsaverage rh --fwhm 14.504073 --C contrast/contrastname.mat --sim mc-z 5000 1.3 f11/csd2 --glmdir f11
--i divided into 5000 each
from above mri_glmfit, i got two files starting with csd1* .csd and csd2*.csd.
Next one is
mri_surfcluster, mri_surfcluster --src contrastname/sig.mgh --csd csd1* .csd --csd csd2* ..csd --sum <text summary file --sum <*.sum> --ocp <*.mgh>
the output file *.sum can be opened in text editor and *.mgh can be seen using tksurfer. Check the link above link for more details (i just followed that link when i did last month).
let me know if you get into more problems.
pratap
On 11/28/2007 07:43 PM, Alex Fornito wrote:
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 mailto:fornitoa@unimelb.edu.au
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
freesurfer@nmr.mgh.harvard.edu
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Alex Fornito