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>

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