Hi Doug, I would ideally like something that is as close as possible to the pcc map that comes out of selxavg3 (the single subject analysis). How is that computed? Thanks, Caspar
On Wednesday, October 9, 2013, Douglas N Greve wrote: > If it is just an effect size you can compute gamma.mgh/rstd.mgh > doug > > On 10/09/2013 01:39 PM, Caspar M. Schwiedrzik wrote: > >> 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 <mailto: >> 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:cschwie...@rockefeller.edu> >> <mailto:cschwie...@rockefeller.edu >> <mailto: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> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto: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> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto: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> >> <mailto:gr >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto: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> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> >> <mailto:gr...@nmr.mgh.harvard.edu >> <m <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel: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>> <tel: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>> >> <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> >> > >> <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> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto: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/> >> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu > > > -- > 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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