On 05/30/2013 04:37 PM, Joseph Dien 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. I don't understand. If you don't have a cluster for a contrast, how are you defining the cluster? From another contrast?
> > 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? What do you mean? The cluster p-value is corrected, why do you need the max p and why does it need to be corrected? > 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? Same as the sign of gamma.mgh > 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?). Some of the BA labels are in FS, but not nearly all of them doug > > 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 > <mailto: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 <mailto: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> >>>>> <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 <mailto: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 <mailto:jdie...@mac.com> >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://joedien.com// >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:jdie...@mac.com> > Phone: 301-226-8848 > Fax: 301-226-8811 > http://joedien.com// > > > > > > > > > > > -- 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
