Hi Doug, I might try to do it in SPM but it requires some more work I think - The Freesurfer retinotopic mapping analysis is automatic and easy to use. Evelina
On Dec 12, 2011, at 10:51 PM, Douglas N Greve wrote: > Hi Evelina, why don't you do the whole analysis in SPM then map the results > to the surface? > doug > > Thunell Evelina wrote: >> >> Hi Douglas, >> >> I do most of my analysis in matlab and SPM. For this one part of my >> experiment - it's a retinotopic mapping that I will use to ensure that my >> ROIs are in V1 - I'm using Freesurfer. I have done slice time correction, >> motion correction and coregistration between functional runs and of the >> structural image already in SPM. I thought that since these flags exist they >> would just skip a step in the processing and send the data directly to the >> next step. But since it's not the case I'll have to do it some other way >> instead, maybe just redo the whole preprocessing in Freesurfer on the >> already preprocessed data. (Running the analysis with selxavg3-sess >> -analysis retlh -s SessXX *-no-preproc *doesn't work.) Anyway, the important >> thing is that the retinotopic mapping data stay coregistered with the rest >> of the functional data. If I can do this step in Freesurfer instead (and the >> rest of the preprocessing) that would be an option. >> >> Thanks a lot, >> Evelina >> >> On Dec 9, 2011, at 7:06 PM, Douglas N Greve wrote: >> >>> Hi Evelina, why do you want to run it without MC? I'm not sure it will run >>> that way. When you run it with -noreg, it causes it not to run the >>> registration. For the preprocessing you have set up, it requires that the >>> registration be run at some point because it needs it to map the fmri to >>> the surface. >>> doug >>> >>> Thunell Evelina wrote: >>>> >>>> Hi, >>>> >>>> Does anyone know how to correctly use the -nomc and -noreg flags? >>>> >>>> When I run: >>>> preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc >>>> I get the error message: >>>> ERROR: could not determine file for >>>> /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr >>>> >>>> I also tried >>>> preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg >>>> which gives the error: >>>> ERROR: cannot find >>>> /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat >>>> Try running register-sess with -per-run >>>> >>>> When I do >>>> preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold >>>> it works fine and finishes without errors (preproc-sess done) >>>> >>>> (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X >>>> 10.6.8) >>>> >>>> Thanks a lot for any help, >>>> Evelina >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto: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 >>> >>> >>> >>> 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. >>> >> > > -- > 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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
