then I get on the order of .02% difference between the contrasted conditions. The run mean values are in my expected ballpark of about 100 or so. The condition betas are just very very small. Or perhaps this is typical of FSFAST analyses?
On Jul 17, 2013, at 2:00 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > The beta's have already been scaled. What do you get if you just > beta/runmean ? > > > > On 07/17/2013 01:45 PM, Joseph Dien wrote: >> I implemented the ROI percent signal change formula following the >> MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values >> I'm getting seem too small (on the order of .0002%). Basically the >> formula is the (beta * peak absolute value of the canonical HRF >> regressor * 100)/(run mean). No derivatives in this case as it is a >> boxcar design. >> >> I took the mean across all the runs since FSFAST uses the same >> regressor across the entire experiment (unlike SPM). >> I used the X.runflac(1).flac.ev(m).Xirf values for the canonical HRF >> as you suggested (where m equals the condition+1). >> >> Is it possible that I'm missing something in the scaling here? >> Especially with a boxcar design, the signal change should be much >> larger than this for a significant cluster, I think. For example, the >> peak HRF value for one of the conditions is 0.0092. If the betas are >> already scaled according to the peak value, then it would come out as >> .02%, which is more reasonable, although still too small. >> >> Thanks for your help with this! >> >> Joe >> >> >> >> On May 31, 2013, at 5:02 PM, Douglas N Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >>> >>> Oh, right, it is probably not there for subcortical. I don't know what I >>> would have to do to write it out. It won't be something that happens >>> before I get back from HBM. Can you remind me after HBM? >>> doug >>> >>> On 05/31/2013 04:44 PM, Joseph Dien wrote: >>>> It looks like the corrected vertex p-values >>>> (ex: cache.th13.abs.sig.voxel.nii.gz) are only available for the >>>> surface-based lh and rh spaces. For the subcortical volume-based >>>> analysis I don't see the corresponding corrected voxel p-values being >>>> available? >>>> >>>> On May 31, 2013, at 2:46 PM, Joseph Dien <jdie...@mac.com >>>> <mailto:jdie...@mac.com> >>>> <mailto:jdie...@mac.com>> wrote: >>>> >>>>> >>>>> On May 31, 2013, at 12:11 PM, Douglas N Greve >>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>>> >>>>>> >>>>>> 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 >>>>> >>>>> Excellent! Thanks! :) >>>>> >>>>>>> >>>>>>> Thanks again for your patience! >>>>>>> >>>>>>> Joe >>>>>>> >>>>>>> On May 30, 2013, at 4:37 PM, Joseph Dien <jdie...@mac.com >>>>>>> <mailto:jdie...@mac.com> >>>>>>> <mailto: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> >>>>>>>> <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> >>>>>>>>>> <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 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> 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: 202-297-8117 >> 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: 202-297-8117 http://joedien.com//
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