Ok, thanks. Then is this command below summarise the best for project on fsaverage and smooth, according to our mails exchange :
*mri_vol2surf --mov **cbf.nii.gz --hemi lh --surf mid --o **lh.fwhm3.fsaverage.cbf.mgh --regheader **subj_id --surf-fwhm 3* --trgsubject fsaverage --icoorder 7 --cortex Best regards, ------------------------------------- Matthieu Vanhoutte, MSc Research Engineer - Department of Neuroradiology Regional University Hospital, Lille, France 2015-03-05 17:24 GMT+01:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > 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 >
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