Also, you can do everything in one vol2surf command with --trgsubject fsaverage. It is identical to doing it in two steps On 03/05/2015 08:12 AM, Matthieu Vanhoutte wrote: > *Update from precedent mail* > > Concerning projection on fsaverage, is it better, worse or equivalent > to do (1) or (2) ? > > (1) > > */# Project and smooth onto anatomical surface/* (--surf mid : mean > surface between pial and white) > > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o > lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint --surf-fwhm 3 > > mris_w_to_curv ////subj_id/ / lh ///lh.fwhm3.cbf.w/ ////lh.fwhm3.cbf// > > *# Resample cbf to fsaverage* > > mri_surf2surf --srcsubject /////subj_id/// --srchemi lh --srcsurfreg > sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg > --sval /////lh.fwhm3.cbf/// --sfmt curv --noreshape --no-cortex --tval > lh.fwhm3.fsaverage.cbf.mgh --tfmt curv/ > > > (2) > > */# Project and smooth onto 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// > / > */# Smooth/* > /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// > / > > Many thanks in advance !! > > Best regards, > > ------------------------------------- > Matthieu Vanhoutte, MSc > Research Engineer - Department of Neuroradiology > Regional University Hospital, Lille, France > > 2015-03-05 14:10 GMT+01:00 Matthieu Vanhoutte > <matthieuvanhou...@gmail.com <mailto:matthieuvanhou...@gmail.com>>: > > Thank you Doug for precisely helping me on smooth detailed command. > > Concerning projection on fsaverage, is it better, worse or > equivalent to do (1) or (2) ? > > (1) > > */# Project and smooth onto anatomical surface/* (--surf mid : > mean surface between pial and white) > > /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o > lh.fwhm3.cbf.w --regheader ///subj_id/ --out_type paint --surf-fwhm 3 > > mris_w_to_curv ////subj_id/ / lh ///lh.fwhm3.cbf.w/ ////lh.fwhm3.cbf// > > mv ${DIR}/surf/lh.fwhm${FWHM}.intensity > ${DIR}/ictus/lh.fwhm${FWHM}.intensity > > rm -f ${DIR}/surf/lh.fwhm${FWHM}.intensity.w > > *# Resample cbf to fsaverage* > > mri_surf2surf --srcsubject /////subj_id/// --srchemi lh > --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh > --trgsurfreg sphere.reg --sval /////lh.fwhm3.cbf/// --sfmt curv > --noreshape --no-cortex --tval lh.fwhm3.fsaverage.cbf.mgh --tfmt curv/ > > > (2) > > */# Project and smooth onto 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// > / > */# Smooth/* > /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// > / > > Many thanks in advance !! > > Best regards, > > ------------------------------------- > Matthieu Vanhoutte, MSc > Research Engineer - Department of Neuroradiology > Regional University Hospital, Lille, France > > 2015-03-02 21:13 GMT+01:00 Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>: > > > 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> > > <mailto: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> > <mailto: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> > <mailto: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 > <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 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > 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
