Run mri_preproc with the -no-subcort-mask option Before you do that, delete the mni305 files in your run directories, otherwise it will not regenerate them.
doug On 08/08/2013 11:17 AM, Emily Boeke wrote: > Hi Doug, > > Thanks for the response. Is this masking out of the cortical regions > in the volume analysis a newer aspect of the processing stream? > Previously I have seen this activation in the volume. > > It would be great if you could let me know the flags to see the full > volume analysis. > > Thanks! > > Emily > > Message: 41 > Date: Wed, 07 Aug 2013 19:29:33 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Different results in surface and volume > analyses > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <5202d85d.1090...@nmr.mgh.harvard.edu > <mailto:5202d85d.1090...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Emily, the processing stream is designed to mask out cortical regions > from the volume analysis. The volume analysis is used for subcortical > structures. To make sure that the same voxels are not analyzed twice, > the cortical surface is masked out of the mni305 analysis. > doug > > ps. If you really want to see the full volume analysis, then there are > some flags that will do this. > > > Message: 14 > Date: Wed, 7 Aug 2013 13:15:37 -0400 > From: Emily Boeke <eboek...@nmr.mgh.harvard.edu > <mailto:eboek...@nmr.mgh.harvard.edu>> > Subject: [Freesurfer] Different results in surface and volume analyses > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <948e8fdf-754a-4ae0-a0c9-86d848f14...@nmr.mgh.harvard.edu > <mailto:948e8fdf-754a-4ae0-a0c9-86d848f14...@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=us-ascii > > Hello everyone, > > I am looking at a visual stimulus vs fixation contrast in my > individual subjects' data to make sure we are seeing normal activation > there. If I look at the surface data in tksurfer, I see activation in > the occipital cortex, but in the mni305 analysis, there is no > activation in this region. > > These are the preprocess , mkanalysis, and selxavg commands I used for > the surface vs. mni305: > > preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down > -surface fsaverage lhrh -mni305-2mm -fsd cond > > mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm > Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 > -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc > down > > mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm > Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 > -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc > down > > mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm > Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 > -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 > -stc down > > selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh > selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh > selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 > > Why might we be seeing this activation on the surface map but not the > volume one? > > Thanks! > Emily > > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 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.
