Hi Doug, this is coming from a seed-based resting state analysis. I would like to show effect size instead of p-values. I thought you calculate them from the slopes or the t-values? Caspar
2013/10/9 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > > Oh, yes, sorry. The reason that mri_glmfit_pcc is failing is because this > is a one-sample group mean (design matrix a column of all 1s). What are you > trying to compute the correlation between? Or do you just want to convert > the p-values to a correlation coefficient? > > > > On 10/09/2013 01:26 PM, Caspar M. Schwiedrzik wrote: > >> Hi Doug, did you already have a chance to look into this? Thanks, Caspar >> >> >> 2013/10/4 Caspar M. Schwiedrzik <cschwie...@rockefeller.edu <mailto: >> cschwiedrz@**rockefeller.edu <cschwie...@rockefeller.edu>>> >> >> >> Done. Thank you very much for looking into this. >> Caspar >> >> >> 2013/10/4 Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> >> Can you tar up you glmfit dir and drop it to me on our file drop? >> >> >> On 10/04/2013 05:29 PM, Caspar M. Schwiedrzik wrote: >> >> Hi Doug, >> >> thank you very much for sending the Matlab function. When >> I run this, it creates a pcc.mgh file for my osgm >> contrast. However, the values seem strange. They range >> from -630 to 36 for my particular dataset. >> I was expecting something between -1 and 1. >> Caspar >> >> >> 2013/10/4 Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >>> >> >> >> I think you are conflating the 1st level and the 2nd >> level. You >> could get pcc out of the 2nd level regardless of what >> you are >> using for the input from the first level. I've >> attached a matlab >> script that will compute the pcc for mri_glmfit output >> >> doug >> >> >> >> On 10/04/2013 03:33 PM, Caspar M. Schwiedrzik wrote: >> >> Hi Doug, >> I guess it boils down to the question how to get a >> group PCC >> map after a RFX GLM? >> Using -m PCC seems to only give me a map per >> subject. Are you >> calculating PCC from the t- values? Thanks, >> Caspar >> >> >> On Thursday, October 3, 2013, Caspar M. >> Schwiedrzik wrote: >> >> Hi Doug, >> >> On Thursday, October 3, 2013, Douglas N Greve >> wrote: >> >> >> It sounds like two issues: >> 1. p-values not consistent with your >> program. What did >> you use >> to compute? Did you do a two-sided (which >> is what >> fsfast uses)? >> >> I used ttest in Matlab, two sided. >> >> 2. Using pcc maps. Why not use -m pcc? >> >> >> Isn't that giving me a map per subject? How do >> I get the >> group map >> that is consistent with the results of >> mri_glmfit run on >> ces.nii? >> >> Thanks, Caspar >> >> >> doug >> >> >> On 10/03/2013 01:10 PM, Caspar M. >> Schwiedrzik wrote: >> >> Hi Doug, >> I loaded the pcc.nii file that I got from >> isxconcat-sess >> into Matlab and then ran a t-test >> against 0 over >> the 4th >> dimension. I converted the resulting >> p-values to >> -log10 >> and then compared them to the output of >> mri_glmfit, namely >> sig.vol. >> This was the mri_glmfit command: >> mri_glmfit \ >> --surf averagesubject hemisphere \ >> --y pcc.nii \ >> --no-cortex \ >> --osgm \ >> --glmdir analysisname >> I was expecting the p-values to be the >> same, which >> apparently is not the case, unless I am >> doing/understanding something wrong. >> >> By now, I am actually more inclined to >> use the >> regression >> coefficients instead. However, I'd >> still like to >> get pcc >> maps from them, if there is a way to >> do so in FSFAST. >> Thanks, Caspar >> >> >> >> >> 2013/10/3 Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >>>> >> >> >> On 10/03/2013 10:39 AM, Caspar M. >> Schwiedrzik >> wrote: >> >> Hi Doug, >> >> when I run a two-tailed t-test >> against 0 >> in Matlab >> on the Rs >> in pcc.nii that I get out of >> isxconcat-sess with >> -m pcc, and >> DOF from ffxdof.dat, I get >> different -log10(p) >> values than the >> ones that come out of mri_glmfit. >> >> I don't understand what you mean. >> Can you >> elaborate? >> >> I am not sure why this is >> happening. >> In principle, I just want pcc >> maps as >> final output >> to show >> them on the surface (instead >> of p-values). >> So I'd >> be happy to >> follow your advice regarding >> the biasing >> effects >> of noise and >> autocorrelation and use the >> regression >> coefficients. However, >> mri_glmfit (v5.1) does not >> seem to output >> pcc maps >> of the >> contrasts (contrary to >> selxavg3-sess on >> the single >> subject >> level). How would I get those? >> >> Thanks, Caspar >> >> >> 2013/10/1 Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> >> <mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >>> >> <mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> >> <mailto: >> gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >>>>> >> >> >> >> On 10/01/2013 01:13 PM, >> Caspar M. >> Schwiedrzik >> wrote: >> > Hi Doug, >> > it would be great if you >> could give >> me some >> further >> advise on the >> > group analysis of functional >> connectivity maps. >> > Specifically, I am >> trying to get PCC >> maps >> for certain >> seeds, and am >> > not planning any >> comparison between >> groups. >> > Following your previous >> advise, I am >> running >> isxconcat-sess with -m >> > pcc to get the PCC maps. >> > I would then run >> > >> > mri_glmfit \ >> > --surf averagesubject >> hemisphere \ >> > --y pcc.nii \ >> > --no-cortex \ >> > --osgm \ >> > --glmdir analysisname >> > >> > *Could you please >> provide some more >> detail >> on what kind of >> analysis is >> > performed when I provide >> pcc.nii as >> an input for >> mri_glmfit? Is it a >> > t-test of the >> Fisher-transformed >> r-values >> against 0? >> I just run a t-test of the >> r-values. I >> don't >> have a >> program to convert >> them to z-values, however, >> there are >> z-values >> that are >> created in the >> first level analysis. >> These are >> generated from the >> p-values but I >> bet it >> would give you the same >> thing. Use -m >> z with >> isxconcat-sess if you >> want >> to use the z. >> > *Is the average r-value >> or z-value saved >> somewhere? >> Which level? For >> mri_glmfit, they are >> not, >> but it is not >> hard to get >> them with matlab. >> > *Do you take the >> autocorrelation into >> account (as in >> Vincent JL et >> > al., 2007. Intrinsic >> functional >> architecture >> in the >> anaesthetized >> > monkey brain. Nature. >> 447:83-86)? >> Not usually, but it could >> be done by >> not including >> -no-whiten when you >> run mkanalysis-sess. I >> usually use the >> regression >> coefficients instead >> of correlation >> coefficients because >> that they >> are at least >> unbiased with >> respect to noise level and >> autocorrelation. >> doug >> >> >> > I'd also be happy to >> look this up >> but I'd >> need to know >> where I can >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> >> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >> >> <tel:617-726-7422>> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> 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<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. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> > >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >
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