Hi Doug, I deleted all old analyses manually, switched to 5.1, redid mkanalysis-sess, mkcontrast-sess, and selxavg3-sess, and still have zeros in the most significant voxels. If there was a bug fix in the meantime, could you please let me know where to obtain it?
The version numbers are the following: mkanalysis-sess v1.64.2.1 mkcontrast-sess v1.17 selxavg3-sess v1.57 fast_selxavg3.m v1.100 Thank you very much! Caspar 2012/11/27 Caspar M. Schwiedrzik <cschwie...@rockefeller.edu>: > 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
