Sounds like a question about a contrast matrix, not a design matrix. What is it that you want to test? If the NULL hypothesis is that the means for each group are the same, then give each group a col in the design matrix, then set up the followin g contrast:

1 -1 0 0
1 0  -1 0
1 0  0 -1

to test for any difference between groups

doug






Alex Fornito wrote:
Hi,
can I ask for some guidance on setting up a design matrix in mri_glmfit to test for a difference anywhere between 4 groups, in a similar vein to an omnibus F-test? I can only think of how to contrast 2 groups, or how to collapse across groups.
Thanks,
A


On 29/12/2007, at 10:31 AM, Alex Fornito wrote:

Thanks, will try it.
Can I ask what the contrast matrix should look like if I want to find regions showing any differences between 4 groups?

I can only think of how I could obtain pairwise differences either between individual groups, or the average of two groups vs that of the other two groups. I would like to compare all groups to each other simultaneously, to identify region where there is at least one difference between any 2 of the 4 groups, as per an F-test.

Thanks again,
Alex


On 26/12/2007, at 4:52 PM, Nick Schmansky wrote:

Alex,

In qdec, currently it's limited to two discrete factors, although using
mri_glmfit (upon which qdec is built) you could formulate your own
contrast matrices having >2 discrete factors.

Nick


On Wed, 2007-12-26 at 13:32 +1100, Alex Fornito wrote:
Great. Thanks for the feedback.


One last question - is it possible to run an analysis with a discrete
variable that has >2 levels? I have four groups I am trying to
compare, and I would like to run an overall analysis akin to an F-test
to see where any differences between them are.
I tried to run this in qdec, but got an error message saying that the
factor must have 2 levels.


Thanks again,
Alex 

On 24/12/2007, at 11:29 AM, Doug Greve wrote:

On Fri, 21 Dec 2007, Alex Fornito wrote:


Hi,
After wrestling with this a bit, I think I get the idea
(finally!). Just to confirm:


1- set a primary threshold in the mri_glmfit command, e.g., --sim
perm 5000 1.3 will run 5000 permutations with the primary cluster
forming threshold set at .05.


This threshold is called the voxel-wise (or vertex-wise) threshold.


2- Look up the cluster summary table and identify clusters with
CWP < .05 (if alpha=.04). These CWP values are corrected based on
the maximal cluster size statistics generated during the
permutations.


3 - Visualize clusters in tksurfer - one way is to load the --
cwsig file, where each cluster is assigned a corrected p-value.
Seeting the overlay display to min=1.3 will then show you all
clusters that are significant at the clusterwise corrected .05
level.


Correct, just keep in mind that the .05 for #3 is the cluster-wise
threshold which is distinct from from the vertex-wise threshold set
in
#1.


Am I right so far?


Couple more questions regarding smoothing:


1 - If I input data obtaioned from qdec into mri_glmfit just to
run the permutations, do I need to specify the --fwhm? Does this
correspond to the one used for the analysis (i.e., the one
specific in qdec), or the residual fwhm obtained from the y.fsgd
file? (Note, I see that you need to specify the residual fwhm for
the monte-carlo sims, by I wanted to check whether a fwhm is
required for the --sim perm option)


it is not required for permutation




2 - does the --var-fwhm option corresond to the variance smoothing
described in the Nichols and Holmes Hum Brain Mapp paper? If so,
it seems this would be useful for --sim perm. Does anyone have any
recommendations for what a good value would be? Should it be the
same fwhm as that used to smooth the thickness values; i.e., is I
specify 15mm in qdec, should I use 15mm for --var-fwhm?


Yes, it does refer to that. I have not really used it much, so I
can't
recommend a fwhm. However, you can be much more agressive with
variance smoothing than for smoothing the raw data. The assumption
with variance smoothing is that the noise variance is constant over
the smoothing kernel.


doug


Thanks again for your help,
Alex




On 11/12/2007, at 12:49 PM, Doug Greve wrote:


Alex Fornito wrote:
Sorry Doug, I'm a bit thick , so pls let me clarify :)
The threshold set in mri_glmfit with --sim perm 5000 1.3
corresponds to the primary (1) vertex-wise threshold; (2) the
cluster-based threshold; or (3) both?
Just #1, the vertex-wise. The simulation is done to figure out
#2.
I'm a little confused, as in you previous response you stated:
Thus, if I set --sim perm 5000 1.3, vertices significant
at p<.05 will first be identified, and those that are
connected will be assigned to clusters.
Correct so far.
But then later said the vertex-wise values are uncorrected. In
that case, and based on your response re: data contained in
the .csd file, I assume that the '1.3' threshold corresponds
to that determined by the permutation distribution for the
group difference statistic at each vertex, rather than the
maxima across all vertices, which corrects for multiple
comparisons as detailed in the Nichols & Holmes (2001) paper.
This is why the vertex-wise values are uncorrected?
The 1.3 is what you determined and specified on the command-
line. The maxima across all vertices is stored in the CSD and
can in principle be used to compute a vertex-wise threshold
(instead of using a cluster-wise correction). In this case, the
1.3 you spec on the cmd line would be meaningless.
If the above is the case, than how and when is the cluster-
wise threshold selected? I noted that you said any cluster-
wise threshold can be selected, by mri_surfcluster does not
allow me to set a --thmin different to that passed to
mri_glmfit when using a .csd file.
By default, mri_surfcluster will print out all clusters along
with their cluster-wise p-value. You then look at the list and
only report the ones that meet the threshold that you feel
comfortable with.
Thanks again.
On 11/12/2007, at 12:03 PM, Doug Greve wrote:
Alex Fornito wrote:
Ok, so sounds like that is not possible - thanks for
clarifying.
I have been playing with the --sim perm option and was
wondering how cluster-level inferences are determined.
From what I understand, a primary (voxel-level) threshold
generally needs to be specified to form clusters, prior to
some statistics assessing a particular property of the
suprathreshold clusters  (e.g., size or mass) being tested
again its null distribution.
I know that the --sim perm requires specification of a
threshold, but I am presuming that this if for cluster-
level inference. mri_surfcluster obtains threshold
information from the .csd file with no further user input,
making me wonder how the 'primary', vertex-level threshold
for determining supra-threshold clusters is set. I see two
possible options:
1 - You are implementing the Threshold-Free Cluster
Enhancement (TFCE) technique described on the Randomize
website.
Never heard of it.
2 - The primary, vertex-wise threshold is determined by
the permutation distribution of the maximal statistic for
the difference between two groups (in a 2-group
comparison). All connected suprathreshold vertices are
then assigned to different clusters, and the size of these
clusters is then tested against the permutation
distribution for cluster size.
Thus, if I set --sim perm 5000 1.3, vertices significant
at p<.05 will first be identified, and those that are
connected will be assigned to clusters.
Correct so far.
Clusters will then be determined significant if p<05, as
evaluated against the permutation distribution for the
maximal cluster size statistic.
You can choose any cluster-wise sig threshold you want (ie,
it is distinct from the vertex-wise threshold).
Is this what the MaxStat and MaxClusterSize columns in
the .csd file correspond to?
I've programmed mri_glmfit to keep track of both the max
cluster size and the maximum statistic. The latter can be
used to do a vertex-wise correction for muliple comparisons
instead of a cluster-wise. This avoids having to set an
arbitrary vertex-wise threshold needed when clustering. I'm
still missing a piece of code that will apply the CSD in
this way.
If this is the case, is using 2 corrected thresholds (for
primary, vertex-wise, and then cluster-level inferences)
seems to be relatively conservative? I have noted that in
many fMR experiments, it seems customary to use an
uncorrected primary threshold based on signal intensity,
coupled with an extent threshold to form clusters, prior
to making FWE-corrected cluster-level inferences.
The vertex-wise theshold is not corrected in any way.
doug
Appreciate help on this and sorry for all the questions -
much of this is new to me!!
Alex
On 07/12/2007, at 5:59 AM, Doug Greve wrote:
FDR assumes that the collection of values has both
positives and negatives. It assumes that the pvalues of
the negatives are uniformly distributed between 0 and 1,
and this model is used to estimate the total number of
positives (both true and false). When you cluster, you
are setting all voxels below a certain threshold to 0,
thus invalidating the assumption about the distribution
of the negatives.
doug
Alexander Fornito wrote:
Sorry, can I ask why the clustering step would
invalidate FDR?
From my understanding, FDR allows you set a limit on
the number of false
positive in a family of contrasts reaching
significance at a nominal
threshold. I would like to this nominal threshold
using cluster stats
(e.g., p<.05, cluster extent 30mm), and then use FDR
to correct for
comparisons at vertices exceeding this initial
threshold, therefore
avoiding running FDR on each vertex of the surface. Is
this not possible?
That does not sound right, I think that the first
clustering step will
probably invalidate FDR. You can use FDR to set the
voxel-wise threshold
when you run mri_surfcluster, but I'm not sure you
can do it afterwards.
Alex Fornito wrote:
I retract the last email - it seems like I was
entering the wrong
sig.mgh file as input. Sorry for the confusion!!!
On a separate issue, I would like to check that I
have the following
correct:
I have extracted a cluster image using
mri_surfcluster withouth
running simulations. Say, for e.g., I use thmin 2
and minarea 30. I
load the resulting output.mgh file into tksurfer.
I would then like to perform FDR correction on the
resulting clusters.
I'm guessing that pressing the FDR button in the
Overlay config menu
will do the trick, since (from what I understand)
the output.mgh file
I have loaded assigns a zero to all vertices not
in a cluster. I
figure that this will therefore result in an FDR
correction that
accounts only for the vertices within my clusters.
However, I'm uncertain how the 'only marked'
checkbox fits in. If I
tick it, I get an error calculating the FDR. I'm
guessing this option
is relevant if you combined a stat map with a
label file.
Am I on the right track?
Thanks again,
Alex
On 05/12/2007, at 9:52 AM, Alex Fornito wrote:
<Pic.png>
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,
FsTutorial_2fGroupAnalysis?
action=highlight&value=fsgd
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
------------------------------------------------------ -------------
-----
_______________________________________________
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
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
<Pic.png>_______________________________________________
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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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
_______________________________________________
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
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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
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
_______________________________________________
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














-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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


_______________________________________________
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










_______________________________________________
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

_______________________________________________
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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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