On 05/31/2013 02:45 PM, Joseph Dien wrote: > > On May 31, 2013, at 12:09 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > >> >> 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? >> > > Well, what the reviewer told me to do is if I present a figure with a > significant cluster for one condition, I should use that as an ROI to > calculate the %age signal change for all four conditions and present > it as a bar chart as part of the figure. I think she wanted to be > able to get a more qualitative sense of the data patterns. If you have a cluster annotation (created by mri_glmfit-sim) then you can apply that to each contrast using mri_segstats with the --annot option.
> >>> >>> 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? > > Well, as I understand it, the drawback of clusterwise statistics is > that while it assures you that the cluster passes muster as not being > due to random chance (at 95% confidence), it doesn't provide any > assurances at the voxel level (or in this case the vertex level) as it > is likely that a cluster is composed of both signal and noise and you > don't know which part is which. So if a cluster covers both BA44 and > BA45 (for example), you can't be sure whether the activation involves > BA44, BA45, or both. A voxelwise correction is more conservative but > if it provides significance, it does allow for this kind of > interpretation. > >>> 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 > > Ah, great! > >>> 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 > > No problem! I worked out that I can use the talairach.nii file made > available by the Talairach Daemon folks. > > >>> >>> 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> >>> <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> >>>>> <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> >>>>>>> <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> >>>>>> <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 >>>>>> <http://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> >>>>> <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> >>>> <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> >>> <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 <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 > > > -------------------------------------------------------------------------------- > > 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
