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 <greve@nmr.mgh.harvard.edu mailto: greve@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 <cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu> <mailto:cschwiedrz@rockefeller.edu <mailto:cschwiedrz@rockefeller.edu>>> Done. Thank you very much for looking into this. Caspar 2013/10/4 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:gr <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> <mailto:greve@nmr.mgh.harvard.edu <m <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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