Hi Doug, I am afraid the p values are still too small in Free Surfer Linux-centos4_x86_64-stable-pub-v5.1.0-full. I redid mkanalysis-sess mkcontrast-sess selxavg3-sess in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in the center of the cluster. Any further advice? Thanks, Caspar
2012/11/26 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > > No, it does not. With version 5 I went to a simple AR1 model instead. > doug > > > > On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote: >> >> Hi Doug, >> thanks for the input. What I meant is that in version 5.1, >> mkanalysis-sess does not seem to recognize the -taumax flag to set the >> maximum delay for the autocorrelation function. >> Caspar >> >> >> 2012/11/26 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>> >>> >>> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote: >>>> >>>> Hi Doug, >>>> I'll do that. >>>> Two quick follow-up questions regarding 5.1: >>>> - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is >>>> there another argument that would allow me to set the autocorrelation? >>> >>> What do you mean by "set the autocorrelation"? You can turn it off with >>> -no-whiten. >>> >>>> - in a block design, would refeventduration be the block length or the >>>> length of the individual events within a block? >>> >>> The block length. This will not change the p-values, only percent signal >>> change values (often not even looked at). >>> doug >>> >>>> Thanks, >>>> Caspar >>>> >>>> 2012/11/26 Douglas N Greve<gr...@nmr.mgh.harvard.edu>: >>>>> >>>>> Hi Caspar, I think I fixed this in later versions. If you upgrade, you >>>>> can run the stats from 5.1 with recons from 4.5 (just don't mix recons >>>>> from different versions). >>>>> doug >>>>> >>>>> On 11/26/2012 01:15 PM, Caspar M. Schwiedrzik wrote: >>>>>> >>>>>> Hi! >>>>>> I ran into a funny problem when calculating contrasts in Freesurfer >>>>>> 4.5.0. >>>>>> Namely, the center of my cluster of significant voxels has a p-value >>>>>> of -0.0, resulting in a funny whole where you would otherwise expect >>>>>> to find the most significant voxel(s). >>>>>> It seems that the p-value is too small. Is there a workaround >>>>>> available? >>>>>> Thank you very much, >>>>>> Caspar >>>>>> _______________________________________________ >>>>>> 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: 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. >>>>> >>> -- >>> 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: 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
