I'm not sure that I understand what I'm looking at. If it is an ROI analysis, then there is no surface, it should be about 40 numbers, one for each ROI.
On 02/03/2015 06:26 PM, Bronwyn Overs wrote: > Hi Doug, > > Thanks for your correction. > > I have now completed the FDR for my case-control comparisons, and it > appears that none of the regions survived. This is again quite > confusing given the large number of parcellated regions that survived > FDR in the SPSS ANCOVA. Can you confirm that this screenshot of the > sig.mgh file from ROI analysis looks as you would expect (it looks > very strange to me): > > > > Kind regards, > > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 > > neura.edu.au <http://neura.edu.au> > > Follow @neuraustralia on twitter > <https://twitter.com/neuraustralia>Follow NeuRA on facebook > <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to > the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> > > On 4/02/2015 9:35 am, Douglas Greve wrote: >> >> Yes, it should be .^ >> >> On 2/3/15 5:33 PM, Bronwyn Overs wrote: >>> Hi Doug, >>> >>> I am having a problem with the line in Matlab 2014b: >>> p = 10^-abs(sigmat); >>> I keep getting the following error: >>> Error using ^ >>> Inputs must be a scalar and a square matrix. >>> To compute elementwise POWER, use POWER (.^) >>> instead. >>> >>> Do you know why this would be? >>> >>> Kind regards, >>> >>> Bronwyn Overs >>> Research Assistant >>> >>> Neuroscience Research Australia >>> >>> Neuroscience Research Australia >>> Margarete Ainsworth Building >>> Barker Street Randwick Sydney NSW 2031 Australia >>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>> >>> neura.edu.au <http://neura.edu.au> >>> >>> Follow @neuraustralia on twitter >>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook >>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to >>> the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe> >>> >>> On 4/02/2015 2:22 am, Douglas Greve wrote: >>>> >>>> There is not a way to do it from the command line. You can do it in >>>> matlab, something like >>>> >>>> sig = MRIread('sig.mgh'); >>>> sigmat = fast_vol2mat(sig); >>>> p = 10^-abs(sigmat); >>>> fdr = .05; >>>> pthresh = fast_fdrthresh(p,fdr); >>>> ind = find(p < pthresh); % This will be a list of ROI indices that >>>> survive FDR >>>> >>>> doug >>>> >>>> On 2/2/15 10:26 PM, Bronwyn Overs wrote: >>>>> Hi Doug, >>>>> >>>>> That makes perfect sense. Just one more thing then, how do you >>>>> conduct an FDR via the command line for an ROI mri_glmfit analysis? >>>>> >>>>> Kind regards, >>>>> >>>>> Bronwyn Overs >>>>> Research Assistant >>>>> >>>>> Neuroscience Research Australia >>>>> >>>>> Neuroscience Research Australia >>>>> Margarete Ainsworth Building >>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>> >>>>> neura.edu.au <http://neura.edu.au> >>>>> >>>>> Follow @neuraustralia on twitter >>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook >>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe >>>>> to the NeuRA Magazine >>>>> <http://www.neura.edu.au/help-research/subscribe> >>>>> >>>>> On 3/02/2015 2:00 pm, Douglas Greve wrote: >>>>>> >>>>>> This is not something you would run the MC sim on because there >>>>>> is no clustering, it is just a list of ROIs with their p-values. >>>>>> The p-values are uncorrected. You can do bonferoni correction >>>>>> across all the ROIs (or just the ones you are interested in). You >>>>>> could do FDR too. >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> On 2/2/15 9:39 PM, Bronwyn Overs wrote: >>>>>>> Thanks Doug, that worked well. >>>>>>> >>>>>>> However, is it possible to run a monte-carlo simulation with >>>>>>> this GLM ROI analysis? I attempted to run it using the following >>>>>>> command... >>>>>>> mri_glmfit-sim --glmdir >>>>>>> DesikanROIAnal_case-control.thick.lh.glmdir --cache 1.3 abs >>>>>>> --cwpvalthresh 0.05 --2spaces >>>>>>> and received the following error: >>>>>>> ERROR: could not determine file for >>>>>>> DesikanROIAnal_case-control.thick.lh.glmdir/mask >>>>>>> >>>>>>> Kind regards, >>>>>>> >>>>>>> Bronwyn Overs >>>>>>> Research Assistant >>>>>>> >>>>>>> Neuroscience Research Australia >>>>>>> >>>>>>> Neuroscience Research Australia >>>>>>> Margarete Ainsworth Building >>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>>> >>>>>>> neura.edu.au <http://neura.edu.au> >>>>>>> >>>>>>> Follow @neuraustralia on twitter >>>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook >>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to >>>>>>> the NeuRA Magazine >>>>>>> <http://www.neura.edu.au/help-research/subscribe> >>>>>>> >>>>>>> On 3/02/2015 11:03 am, Douglas Greve wrote: >>>>>>>> >>>>>>>> Even easier. Run aparcstats2table, then run mri_glmfit passing >>>>>>>> the output of aparcstats2table with --table (instead of --y). >>>>>>>> There's something on the wiki about it, also look for the ROI >>>>>>>> tutorial. >>>>>>>> doug >>>>>>>> >>>>>>>> >>>>>>>> On 2/2/15 6:20 PM, Bronwyn Overs wrote: >>>>>>>>> Hi Doug, >>>>>>>>> >>>>>>>>> I am not sure how to run an ROI analysis using mri_glmfit. Is >>>>>>>>> there a wiki page detailing this method (I was unable to find >>>>>>>>> one)? Is the first step to map lh.aparc.label and >>>>>>>>> rh.aparc.label from fsaverage to each of my individual >>>>>>>>> subjects using mri_label2label? When I do so and then view the >>>>>>>>> mapped label for an individual subject in freeview, it appears >>>>>>>>> to be a continuous label for all of the parcellated regions >>>>>>>>> combined. Is this correct? >>>>>>>>> >>>>>>>>> Kind regards, >>>>>>>>> >>>>>>>>> Bronwyn Overs >>>>>>>>> Research Assistant >>>>>>>>> >>>>>>>>> Neuroscience Research Australia >>>>>>>>> >>>>>>>>> Neuroscience Research Australia >>>>>>>>> Margarete Ainsworth Building >>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>>>>> >>>>>>>>> neura.edu.au <http://neura.edu.au> >>>>>>>>> >>>>>>>>> Follow @neuraustralia on twitter >>>>>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook >>>>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe >>>>>>>>> to the NeuRA Magazine >>>>>>>>> <http://www.neura.edu.au/help-research/subscribe> >>>>>>>>> >>>>>>>>> On 3/02/2015 3:31 am, Douglas Greve wrote: >>>>>>>>>> >>>>>>>>>> First, I would run the ROI analysis in mri_glmfit to see if >>>>>>>>>> you get the same results as in SPSS. In the handfull of these >>>>>>>>>> cases, no one has been able to correctly replicate the FS >>>>>>>>>> design matrix in SPSS, so I suspect that is part of the >>>>>>>>>> discrepancy. The other thing is that ROI and vertex-wise >>>>>>>>>> analyses are simply different. As an extreme example, if some >>>>>>>>>> of the vertices are pos and some are neg then they would >>>>>>>>>> cancel out when you average them in an ROI but individually >>>>>>>>>> could be significant at the vertex level. If you analyze the >>>>>>>>>> average over the cluster then that should come out as >>>>>>>>>> significant. >>>>>>>>>> >>>>>>>>>> doug >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 2/1/15 11:36 PM, Bronwyn Overs wrote: >>>>>>>>>>> Dear FreeSurfer Mailing List, >>>>>>>>>>> >>>>>>>>>>> I have a sample of schizophrenia and control subjects for >>>>>>>>>>> whom I have run a case-control analysis of cortical >>>>>>>>>>> thickness using two separate methods (GLM vertex-wise >>>>>>>>>>> analysis in freesurfer, repeated measures ANCOVA analysis of >>>>>>>>>>> parcellated data in SPSS). However, for each methods of >>>>>>>>>>> analysis I am getting extremely different results. For the >>>>>>>>>>> GLM in Freesurfer I have only 1 small cluster in the frontal >>>>>>>>>>> lobe that differs between cases and controls (controlling >>>>>>>>>>> for all other IVs, FWMH = 10mm, cluster-forming threshold= >>>>>>>>>>> .05, cluster-wise pval=.05), while for the ANCOVA method all >>>>>>>>>>> but 8 of the parcellated regions differ significantly >>>>>>>>>>> between groups (p<.05). For both methods I have used the >>>>>>>>>>> same model of predictors (independent variables = gender, >>>>>>>>>>> group, scanning site; covariate = age) and exactly the same >>>>>>>>>>> sample of participants. I have also replicated the GLM >>>>>>>>>>> analysis using the QDEC GUI to ensure that I had no made any >>>>>>>>>>> mistakes. >>>>>>>>>>> >>>>>>>>>>> Can you provide any insight into why I would be seeing such >>>>>>>>>>> different results for each method using the same data set? >>>>>>>>>>> My findings using the ANCOVA analysis make much more sense >>>>>>>>>>> to me, given previous findings of reduced cortical thickness >>>>>>>>>>> in schizophrenia subjects. I was surprised not to find the >>>>>>>>>>> same pattern of effects using the GLM analysis. >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> Kind regards, >>>>>>>>>>> >>>>>>>>>>> Bronwyn Overs >>>>>>>>>>> Research Assistant >>>>>>>>>>> >>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>> >>>>>>>>>>> Neuroscience Research Australia >>>>>>>>>>> Margarete Ainsworth Building >>>>>>>>>>> Barker Street Randwick Sydney NSW 2031 Australia >>>>>>>>>>> *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 >>>>>>>>>>> >>>>>>>>>>> neura.edu.au <http://neura.edu.au> >>>>>>>>>>> >>>>>>>>>>> Follow @neuraustralia on twitter >>>>>>>>>>> <https://twitter.com/neuraustralia>Follow NeuRA on facebook >>>>>>>>>>> <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe >>>>>>>>>>> to the NeuRA Magazine >>>>>>>>>>> <http://www.neura.edu.au/help-research/subscribe> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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. >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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. >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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. >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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. >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> _______________________________________________ >> 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. > > > > _______________________________________________ > 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 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
