I was able to make more progress so I'm mostly good at this point but I have a remaining question:
I assume the contents of sig.nii.gz (which I assume are the vertex p-values) are not FWE corrected. Is it possible to get FWE-corrected vertex p-values? Or are only clusterwise corrections available? Thanks again for your patience! Joe On May 30, 2013, at 4:37 PM, Joseph Dien <jdie...@mac.com> wrote: > Just to make sure I'm doing this right, I'm going to summarize what I've > taken away from your answers and to ask some new questions. In order to > present the results, I need two things: > > 1) A set of histograms (with error bars) for each cluster figure to show the > % signal change for each of the four contrasts of interest. > The cache.th20.pos.y.ocn.dat file only gives it for the condition where the > cluster was significant so I can't use that. > So I could use mri_label2vol to convert cache.th20.neg.sig.ocn.annot from the > group level analysis to generate a mask for each cluster of interest. > Then I could extract the value of the voxels from each subject's cespct file > for each contrast, average them across the cluster ROI, then average them > across each subject, to generate the histogram? > This would suffice to give me the %age signal change? > I would be doing these computations in Matlab using MRIread. > > 2) A results table with the headings: > > Cluster p (FWE corrected) > Cluster size > Peak Voxel p (FWE corrected) > Peak Voxel T > Peak Voxel Coords > BA > Anatomical Landmark > > I can get the first two from the cache.th20.pos/neg.sig.cluster.summary files > from the group level analysis. > I can get the peak voxel coordinates from the summary files as well. > I can use this to get the peak voxel p from the group level sig.nii.gz file. > Is this FWE corrected? If not, how can I get this information? > I can use these coordinates to get the peak voxel T by getting the value from > the group level F.nii.gz file and taking its square root. How can I get the > sign of the T statistic? > I can use the Lancaster transform to convert the MNI305 peak voxel > coordinates into the Atlas coordinates to look up the putative BA and > landmarks (unless there is a better way with Freesurfer? I'm seeing some > references to some BA labels in the forum but it doesn't look like this is a > complete set yet?). > > Sorry for all these questions! I got some nice results from FSFAST and would > like to get them written up. > > Cheers! > > Joe > > > > > On May 29, 2013, at 10:53 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > >> >> On 5/29/13 10:42 PM, Joseph Dien wrote: >>> >>> On May 29, 2013, at 11:40 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> wrote: >>> >>>> Hi Joe, >>>> >>>> On 05/29/2013 01:00 AM, Joseph Dien wrote: >>>>> I need to extract the beta weights from a cluster identified with >>>>> FS-Fast in order to compute percentage signal change. >>>>> >>>>> 1) I see a file called beta.nii.gz that appears to have the beta >>>>> weight information. It has a four dimensional structure and the >>>>> fourth dimension appears to be the beta weights. Is there an index >>>>> somewhere as to which beta weight is which? Or if not, how are they >>>>> organized? >>>> For the first level analysis, the first N beta weights correspond to the >>>> N conditions in the paradigm file. The rest are nuisance variables. >>>>> >>> >>> Ah, very good! In order to compute the percent signal change statistic >>> (I'm following the MarsBaR approach: >>> http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) >>> I'm also going to need the beta weights for the session mean regressors. >>> How are the nuisance regressors organized? >> You can just use the meanfunc.nii.gz. Also, each contrasts is computed as >> the simple contrast (ces) and as a percent of the baseline at the voxel >> (cespct, cesvarpct). >>> >>>>> 2) In order to extract the cluster, it looks like I would >>>>> use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a >>>>> volume where the voxels are tagged with the number of the >>>>> corresponding cluster. >>>> Is that from a group analysis? >>>>> >>> >>> Yes, that's right. >>> >>>>> I could then use that to generate masks to extract the information I >>>>> need for each cluster from beta.nii.gz. >>>> If this is from a group analysis, then there should already be a file >>>> there (something.y.ocn.dat) that has a value for each subject in the >>>> rows and a value for each cluster in the columns. >>>>> >>> >>> I see it. Are these values already scaled as percent signal change? If >>> so, that would be wonderful! :) >> Only if you specified it when you ran isxconcat-sess. Note that the >> "non-scaled" values are actually scaled to percent of grand mean intensity. >>> >>>>> Is that correct? >>>>> >>>>> 3) The final information that I would need is the canonical hrf shape >>>>> generated by FSFAST for a single event. I guess I could generate that >>>>> by setting up a dummy analysis run with a single event of the desired >>>>> duration and then look in the X variable in the resulting X.mat file? >>>> try this >>>> plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf) >>>>> >>> >>> Perfect! :) >>> >>>>> Sorry for all the questions! >>>>> >>>>> Joe >>>>> >>>>> >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> >>>>> Joseph Dien, >>>>> Senior Research Scientist >>>>> University of Maryland >>>>> >>>>> E-mail: jdie...@mac.com <mailto:jdie...@mac.com> >>>>> Phone: 301-226-8848 >>>>> Fax: 301-226-8811 >>>>> http://joedien.com// >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> gr...@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom it >>>> is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you in >>>> error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien, >>> Senior Research Scientist >>> University of Maryland >>> >>> E-mail: jdie...@mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > > > -------------------------------------------------------------------------------- > > Joseph Dien, > Senior Research Scientist > University of Maryland > > E-mail: jdie...@mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//
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