w format is the paint format output from your vol2surf command. We tend not to use either w or curv formats anymore On 03/05/2015 11:19 AM, Matthieu Vanhoutte wrote: > I don't know if we are talking about the same thing. > > In precedent mail you told me solution #1 was better : > > */# 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 > > > / > But you told me : > /BTW, why are you changing format from w to curv? > Why use curv at all? I'd use mgz or nifti. > > / > At this point I don't know what this means ? > > Thanks, > > Matthieu > > 2015-03-05 17:12 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > > > Just add --trgsubject fsaverage to the mri_vol2surf command line. Run > mri_vol2surf with --help to get more info > > On 03/05/2015 10:52 AM, Matthieu Vanhoutte wrote: > > Thank you Douglas but I don't understand the solution you propose. > > Could you please show me the command lines ? > > > > ------------------------------------- > > Matthieu Vanhoutte, MSc > > Research Engineer - Department of Neuroradiology > > Regional University Hospital, Lille, France > > > > 2015-03-05 16:45 GMT+01:00 Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>>: > > > > > > > > #1 is probably better. BTW, why are you changing format from > w to > > curv? > > Why use curv at all? I'd use mgz or nifti. > > > > > > > > On 03/05/2015 08:10 AM, Matthieu Vanhoutte wrote: > > > 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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto: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>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> > > > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > > <mailto: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>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto: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>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto: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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto: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 > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> > > > Phone Number:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> <tel:617-726-7422 <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://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> > > <http://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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto: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 > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > > <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> > <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> > > 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 > <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
