You can try specifying the functional stem in mkanalysis-sess with -funcstem yourfuncstem (assuming your data are yourfuncstem.nii). This will cause selxavg3-sess to bypass the preprocessing. doug
Thunell Evelina wrote: > 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 >> >> > > > > -- 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
