it does not look like you changed the command line. Also, please cut and paste the info into the email instead of taking a snapshot. thanks doug
On 02/04/2013 07:26 AM, Richter, Julia wrote: > This doesn't work either (see attachment) :( > > -----Ursprüngliche Nachricht----- > Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Gesendet: Donnerstag, 31. Januar 2013 20:29 > An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu > Betreff: Re: AW: [Freesurfer] mean cortical thickness of significant clusters > in qdec > > 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
