Hi Suzanne, why would you not just re-run mri_glmfit-sim with the
different vertex wise threshold? If you want to use 20 voxels, then
you'd have to look a the table and see what cluster p-value that
corresponds to with vertex threshold = .005
doug
On 9/11/13 10:20 AM, Suzanne Oosterwijk wrote:
Hi Doug,
Thanks for your reply. I know how to run mri_glmfit-sim. What I'd like
to do is to apply a more liberal threshold to my data to examine the
clusters that fall outside of the MC-corrected threshold. To do this I
applied the mri_surfcluster command with a vertex-wise threshold of p
< .005, and a minarea of 50 mm2. My question is how I should interpret
the minarea flag. I want to have some insight in whether this
threshold is more liberal than a threshold of 20 continuous voxels
with a p-value of .005 (p < .005; k > 20) or whether this threshold is
more conservative.
Thanks,
Suzanne
On Wed, Sep 11, 2013 at 12:08 AM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
Hi Suzanne, I'll cc the FS list so others can benefit ...
On 09/09/2013 06:02 AM, Suzanne Oosterwijk wrote:
Hi Doug,
I have two follow-up questions to enhance my own understanding
of Freesurfer. I know that MC simulations take into account
the smoothness of the data. I noticed that the smoothing
factor of my surface maps is quite high (around 8/9 fwhm),
even though I applied a smoothing factor of 5 during
pre-processing. Can you explain to me why the final maps have
such a high fwhm? Is this because of the transformations that
are necessary to create the surfaces?
The final measured FWHM is a composite of the smoothing you
applied plus any smoothness that may already be in the data. Eg,
when the surfaces are created, there is a smoothness constraint
that can cause smoothness in the surfaces. The gyrification index
has very high smoothenss. For fMRI, there is already natural
smoothness in the data plus smoothness added due to interpolation
when sampling to the surface.
Another question concerns the relationship between voxels and
vertices. Does one voxel corresponds to one vertex, or is the
relationship different? This may be a very stupid question,
but I thoroughly searched the wiki and the web without finding
a straightforward answer.
Vertices and voxels are different entities. A voxel is a 3D box, a
vertex is essentially a 2D triangle on the surface. The surface is
made from a volume, of course. Initially, the square face of a
voxel is divided into two triangles of equal size. The location of
the vertices are then adjusted to get a better fit. Oftentimes, we
use the term voxel and vertex interchangeably because each just
represents a data point either on the surface or in the volume.
The next question is, if I want to apply a liberal threshold
to my data that is similar to say p < .005; k > 20, then how
do I produce this using the minarea flag in the
mri_surfcluster command?
I'm not sure what you mean by p < .005. Is that a vertex-wise
threshold (ie, the cluster-forming threshold) or cluster-wise?
What is k? If you want to correct for multiple comparisons, then
you can run mri_glmfit-sim. Once you select a cluster-wise and
cluster-forming thresholds (and given the FWHM and search space),
the critical clustersize can be determined.
doug
Thanks in advance for your answers!
Suzanne
On Tue, Sep 3, 2013 at 3:57 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
Hi Suzanne, the pre-computed data is for a full
hemisphere. if you
have
a smaller search space, then the whole hemi results will
be too
conservative. In that case, you should run mri_glmfit-sim
without the
--cache and with --sim as indicated in your command line
(which looks
correct to me). The simulations can take a while. If you
send me your
label, I can compute cached tables for you, so you don't
have to keep
running 10000 iterations of mri_glmfit-sim
doug
On 09/02/2013 12:04 PM, Suzanne Oosterwijk wrote:
> [Attachment(s) <#TopText> from Suzanne Oosterwijk
included below]
>
> Hi all,
>
> I have a question about the Monte Carlo simulation in
Freesurfer. I
> would like to run a simulation to define the minimum cluster
size in a
> specific collection of vertices (say within a ROI
label). After
> running a masked glmfit the pre-cached simulation
doesn’t seem to
> correct for the smaller number of vertices; the text files
produce the
> same results. I also ran a full simulation to see
whether that
made a
> difference, and then I got different results. I just want to
make sure
> that this is because the smaller volume was applied and
not simply
> because the “real” simulation can differ from the
pre-cached data.
> Attached are the different output files, the cached MC with
mask, the
> cached MC without mask, the simulation with mask and a
normal
cluster
> search within the mask (which demonstrates that there are
> sub-threshold clusters).
>
> Below is my code,
>
> foreach s (f_fear_c_fear f_disg_c_disg f_mf_c_mf
f_notc_c_notc)
>
> pushd ${s}
>
> mri_glmfit --surf fsaverage lh --y ces.nii.gz --osgm
--glmdir
> glm.masked --label
>
/home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/network_labels/FP_DN_network.label
>
> mri_glmfit-sim --cache 2.3 pos --sim-sign pos
--cwpvalthresh .05
> --glmdir glm.masked
>
> mri_surfcluster --sign pos --hemi lh --in
glm.masked/osgm/sig.mgh
> --thmin 2.3 --thmax infinity --minarea 50 --subject
fsaverage --sum
> glm.masked/osgm/cluster_pos_23.sum --o
> ./glm.masked/osgm/sig.cluster_pos_23.mgh --annot aparc
>
> cd ..
>
> end
>
>
> I used this code to run the simulation:
>
> mri_glmfit-sim --glmdir glm.masked --sim mc-z 10000 2.3
mc-z.pos.23
> --sim-sign pos
>
> Thanks in advance for responding!
>
> Suzanne
>
--
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MGH-NMR Center
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>
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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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Outgoing:
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--
Suzanne Oosterwijk, Ph.D.
Postdoctoral Researcher
Department of Social Psychology
University of Amsterdam
s.oosterwijk@u <mailto:s.oosterw...@neu.edu>va.nl <http://va.nl>
https://sites.google.com/site/suzanneoosterwijk/
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