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 > 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<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 >> > >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. 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Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > -- Suzanne Oosterwijk, Ph.D. Postdoctoral Researcher Department of Social Psychology University of Amsterdam s.oosterwijk@u <s.oosterw...@neu.edu>va.nl https://sites.google.com/site/suzanneoosterwijk/
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