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
