Anyone know how to reset the LOCAL? Even if temporarily to see if this is the problem? doug
On 02/12/2013 08:23 AM, Richter, Julia wrote: > It says the same even if I put 1.3 in quotes. :( Any other possibility to get > access to the data? > > > -----Ursprüngliche Nachricht----- > Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Gesendet: Montag, 11. Februar 2013 19:04 > An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu > Betreff: Re: AW: AW: AW: [Freesurfer] mean cortical thickness of significant > clusters in qdec > > > It may be a German operating system replacing 1.3 with 1,3. Maybe put it in > quotes, ie, "1.3" > > On 02/11/2013 04:17 AM, Richter, Julia wrote: >> Dear Doug, >> >> this is what appears when I type my command in the command window: >> >> mri_glmfit-sim --cache 1.3 abs --cwpvalthresh .99 >> ERROR: thresh 1,3, must be 1.3, 2.0, 3.0, 3.3, 4.0 >> >> That's it...Any ideas why this is happening? >> >> Many thanks in advance! >> >> Best, Julia >> >> -----Ursprüngliche Nachricht----- >> Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >> Gesendet: Donnerstag, 7. Februar 2013 17:32 >> An: Richter, Julia; Freesurfer@nmr.mgh.harvard.edu >> Betreff: Re: AW: AW: [Freesurfer] mean cortical thickness of >> significant clusters in qdec >> >> 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/ >> >> >> > -- > 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/ > > > -- 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
