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>> wrote: > >> >> On May 31, 2013, at 12:11 PM, Douglas N Greve >> <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>> 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>> 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 >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> > > > > > > > > > > > -- 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 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.
