On 05/31/2013 01:49 AM, Joseph Dien wrote: > 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? There should be something like cache.th13.abs.sig.voxel.mgh which is corrected on a voxelwise basis (the th13 is just part of the name but it should be the same regardless of the threshold you choose) doug > > Thanks again for your patience! > > Joe > > On May 30, 2013, at 4:37 PM, Joseph Dien <jdie...@mac.com > <mailto: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 <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// >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> 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
