The threshold must be in the form of -log10(pthreshold). So, if you want pthreshold=.05, then use 1.3 doug
On 01/31/2013 07:37 AM, Richter, Julia wrote: > Dear Doug, > > thanks for your reply. I tried the command you suggested, but I always get an > error message that there is something wrong with my threshold. I took a > screenshot of the command window and attached it to this mail. I will be very > happy if you have a look at it. > > Looking forward to your answer, > > Best, Julia > > -----Ursprüngliche Nachricht----- > Von: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve > Gesendet: Mittwoch, 30. Januar 2013 17:16 > An: Richter, Julia; free surfer > Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in > qdec > > Oh, sorry, I thought you said you were using mri_glmfit-sim (which does not > have an FDR option). Are you using the FDR in QDEC? If so, it will display > the voxel-wise threshold that realizes the FDR threshold. You can then run > mri_glmfit-sim --cache threshold sign --cwpvalthresh .99 where threshold is > the voxelwise threshold from FDR and sign is either abs (absolute), pos, or > neg. Setting cwpvalthresh=.99 tell it to report all clusters > > doug > > On 1/30/13 8:09 AM, Richter, Julia wrote: >> No it is not...or I just do not find it. >> >> Might it be that I only get the xxx.y.ocn.dat if I correct for multiple >> comparisons with Monte Carlo? If yes, is there any possibility that I get >> this xxx.y.ocn.dat when correcting with FDR? >> >> Many thanks, Julia >> >> -----Ursprüngliche Nachricht----- >> Von: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N >> Greve >> Gesendet: Dienstag, 29. Januar 2013 18:46 >> An: freesurfer@nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] mean cortical thickness of significant clusters in >> qdec >> >> Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not? >> doug >> >> >> On 01/29/2013 11:03 AM, Richter, Julia wrote: >>> Dear FreeSurfer experts, >>> >>> I did a group analysis in qdec, found several significant clusters and >>> would now like to extract the mean cortical thickness of each >>> significant cluster. I know that I have to run mri_glmfit-sim to do >>> this, but I do not understand which commands I need to get the >>> xxx.y.ocn.dat as output by running mri_glmfit-sim. >>> >>> Any ideas? Any help is appreciated. J >>> >>> Best wishes, Julia >>> >>> >>> >>> _______________________________________________ >>> 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. >> >> >> > _______________________________________________ > 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
