I noticed that you are using contrasts.sig.mgh as the input to mri_surfcluster and that the source frame is 0. contrasts.sig.mgh will have many frames. Does the 1st frame (frame 0) correspond to the image below? If not, then add --frame frameno  to your cmd where frameno is the 0-based frame number that corresponds to that image.

doug

Alex Fornito wrote:
3dcopy gefunct1.nii gefunct1

Thanks for all your help guys, but I am still having trouble (!). This time I've tried a different dataset, again just a simple 2 group comaprison with no covariates.

Running this in qdec, and visualizing with a low threshold (min=1.3), I see a whole bunch of clusters (see attached). However, when I run mri_surfcluster, I only get one whole brain cluster again (see below). This time I smoothed with 15 mm in qdec, although I get the same if I smooth with 10mm. I have kept the thresholds low on purpose, because I expect that something should come out?? I did not run simulations in this instance, to cut processing time.

mri_surfcluster --in qdec/MF_lh_15mm/contrasts.sig.mgh  --no-adjust --subject fsaverage/ --hemi l h --thmin 1.3 --minarea 15 --sum TestClusters

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_lh_15mm/contrasts.sig.mgh paint
srcsubjid      = fsaverage/
srcsurf        = white
srcframe       = 0
thsign         = abs
thmin          = 1.3
thmax          = -1
fdr            = -1
minarea        = 15
xfmfile        = talairach.xfm
nth         = -1
sumfile  = TestClusters
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/t alairach.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/fsav erage//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/fsa verage//surf/lh.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 = 1e+10 at vertex 26
overall min = 1.75775 at vertex 126983
surface nvertices 163842
surface area 65416.985991
surface area 65416.985976
NOT Adjusting threshold for 1-tailed test
Searching for Clusters ...
thmin=1.300000 (1.300000), thmax=-1.000000 (-1), thsignid=0, minarea=15.000000
Found 1 clusters
Max cluster size 103339.460938
INFO: fixing MNI talairach coordinates




On 05/12/2007, at 4:19 AM, Doug Greve wrote:

There's really no such thing as an opt kernel size. The best size depends on the underlying signal and can be space variant.

doug

Alex Fornito wrote:
Yes, I selected 25 mm on qdec, based on the Lerch paper suggesting this was a generally 'optimal' kernel size. The 34.309.. was the residual output to y.fsgd.

Do you recommend a smaller kernel?


On 04/12/2007, at 5:41 PM, Pratap Kunwar wrote:

I think, one reason for getting only one big cluster is because your fwhm
value is very high. By the way how did you get fwhm 34.309616??, was it
produced by selecting fwhm 25 (max on Qdec)on Qdec?

Did you try fwhm 10 or 15?

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.
---> i had split simulation (10,000 iterations)into multiple runs csd1*
(5000 iterations) and csd2* (5000 iterations) since mc-z  relatively takes
long time comparing to permutation.
More on,
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
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





-------------------------------------------------------------------
-----

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Freesurfer mailing list



_______________________________________________
Freesurfer mailing list





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








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




 


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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




 


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting