On May 31, 2013, at 12:09 PM, Douglas N Greve <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. >> >> 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>> 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 -------------------------------------------------------------------------------- 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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