On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote: > Dear Doug, > > Thank you for helping ! > > Yes I directly used the regheader option because in the steps before I > already registered ASL maps on anatomical T1. > > The brain.fsaverage.lh.mgh come from the projection of the T1 brain > mask (dilated by 1) on the fsaverage. > > 1) So isn't it better to project first on the anatomical subject then > on fsaverage than what I've done ? This is what is done internally when you spec a target subject that is not the same as the source subject. > > 2) Smoothing with mris_fwhm is a good way with --mask option ? Yes, though I don't think that masking will have an effect the way you created the mask (everything will be in the mask). I would use --cortex to smooth only within cortex (and so exclude the medial wall). doug
> > Thank you for your precious advices ! > > Best regards, > > ------------------------------------- > Matthieu Vanhoutte, MSc > Research Engineer - Department of Neuroradiology > Regional University Hospital, Lille, France > > 2015-03-01 19:45 GMT+01:00 Douglas Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > > > Basically looks ok. The only things that jump out at me are that > you are using regheader (I would create a registration file with > bbregister rather than assuming that there was no motion between > the anatomical and the ASL). Where did brain.fsaverage.lh.mgh come > from? > doug > > > > On 2/27/15 2:16 PM, Matthieu Vanhoutte wrote: >> Dear Freesurfer's experts, >> >> I computed some perfusion maps from ASL data. These perfusion >> maps were registered on anatomical T1 and I would like to make a >> group analysis on surfaces. Please find below my actual commands >> in order to project these volumic maps on fsaverage then smooth >> the data projected on fsaverage : >> >> *Project CBF maps on fsaverage* : >> /mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject >> fsaverage --interp trilin --projfrac 0.5 --hemi lh --o >> lh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg// >> //mri_vol2surf --mov cbf.nii.gz --regheader subj_id--trgsubject >> fsaverage --interp trilin --projfrac 0.5 --hemi rh --o >> rh.fsaverage.cbf.mgh --noreshape --cortex --surfreg sphere.reg/ >> >> *Smooth the data projected on fsaverage (native ASL data size >> voxel of 3mm)* : >> /mris_fwhm --s fsaverage --hemi lh --smooth-only --i >> lh.fsaverage.cbf.mgh --fwhm 3 --o lh.fwhm3.fsaverage.cbf.mgh >> --mask brain.fsaverage.lh.mgh// >> //mris_fwhm --s fsaverage --hemi rh --smooth-only --i >> rh.fsaverage.cbf.mgh --fwhm 3 --o rh.fwhm3.fsaverage.cbf.mgh >> --mask brain.fsaverage.rh.mgh/ >> >> Could you advise me on these two steps and tell me first if this >> is the best way to project CBF maps on fsaverage, then to smooth >> the data on surfaces ? Is my process could be improved ? >> >> Best regards, >> -- >> ----------------------------- >> Matthieu Vanhoutte, MSc >> Research Engineer - Department of Neuroradiology >> Regional University Hospital, Lille, France >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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: 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
