subject:"Re\: \[Freesurfer\] Projection of CBF maps on fsaverage and smooth"

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Douglas N Greve


Yes. You don't want to sample at the white because you'll get large 
partial volume effects. The mid is better. Having said that, I don't see 
large differences in fMRI at typical voxel sizes ~3mm

doug

On 03/05/2015 12:27 PM, Matthieu Vanhoutte wrote:
> Many thanks Doug !
>
> Last point of vue concerning the command : is the --surf mid (mean 
> surface between pial and white) better than default white ?
>
> /mri_vol2surf --mov ///cbf.nii.gz/ --hemi lh --surf mid --o 
> //lh.fwhm3.fsaverage.cbf.mgh --regheader ///subj_id/ --surf-fwhm 3/ 
> --trgsubject fsaverage --cortex
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-05 18:23 GMT+01:00 Douglas N Greve  >:
>
>
> The icoorder is only needed if you don't have a target subject.
>
> To do your group analysis, you can just run mri_concat, eg,
>
> mri_concat subject1/lh.fwhm3.fsaverage.cbf.mgh
> subject2/lh.fwhm3.fsaverage.cbf.mgh --o
> all.subjects.lh.fwhm3.fsaverage.cbf.mgh
>
> Then use all.subjects.lh.fwhm3.fsaverage.cbf.mgh as input to
> mri_glmfit
>
>
>
>
> On 03/05/2015 12:16 PM, Matthieu Vanhoutte wrote:
> > Thanks !
> >
> > Why remove icoorder because it was suggested in the mri_vol2surf
> > --help examples ?
> >
> > May I ask you a last question : I want to make a group analyse with
> > freesurfer tools. With these CBF projected on fsaverage and smooth
> > (with the last command line), could I do as if my data were
> previously
> > cached (qcached) and use the "mri_preproc --cache-in" command ?
> >
> > Best regards,
> >
> > -
> > Matthieu Vanhoutte, MSc
> > Research Engineer - Department of Neuroradiology
> > Regional University Hospital, Lille, France
> >
> > 2015-03-05 18:02 GMT+01:00 Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>
> >  >>:
> >
> > yes, but remove icoorder
> >
> > On 03/05/2015 11:50 AM, Matthieu Vanhoutte wrote:
> > > 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
> >  
> >
> > >  
> >   > >
> > > 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

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Douglas N Greve


The icoorder is only needed if you don't have a target subject.

To do your group analysis, you can just run mri_concat, eg,

mri_concat subject1/lh.fwhm3.fsaverage.cbf.mgh 
subject2/lh.fwhm3.fsaverage.cbf.mgh --o 
all.subjects.lh.fwhm3.fsaverage.cbf.mgh

Then use all.subjects.lh.fwhm3.fsaverage.cbf.mgh as input to mri_glmfit




On 03/05/2015 12:16 PM, Matthieu Vanhoutte wrote:
> Thanks !
>
> Why remove icoorder because it was suggested in the mri_vol2surf 
> --help examples ?
>
> May I ask you a last question : I want to make a group analyse with 
> freesurfer tools. With these CBF projected on fsaverage and smooth 
> (with the last command line), could I do as if my data were previously 
> cached (qcached) and use the "mri_preproc --cache-in" command ?
>
> Best regards,
>
> -
> Matthieu Vanhoutte, MSc
> Research Engineer - Department of Neuroradiology
> Regional University Hospital, Lille, France
>
> 2015-03-05 18:02 GMT+01:00 Douglas N Greve  >:
>
> yes, but remove icoorder
>
> On 03/05/2015 11:50 AM, Matthieu Vanhoutte wrote:
> > 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
> mailto: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
> >  
> >
> > >  
> >   > >
> > >
> > > 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
> > >  
> >  >
> >  
> >>
> > > >

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Matthieu Vanhoutte

Thanks !

Why remove icoorder because it was suggested in the mri_vol2surf --help
examples ?

May I ask you a last question : I want to make a group analyse with
freesurfer tools. With these CBF projected on fsaverage and smooth (with
the last command line), could I do as if my data were previously cached
(qcached) and use the "mri_preproc --cache-in" command ?

Best regards,

-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France

2015-03-05 18:02 GMT+01:00 Douglas N Greve :

> yes, but remove icoorder
>
> On 03/05/2015 11:50 AM, Matthieu Vanhoutte wrote:
> > 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  > >:
> >
> > 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
> > 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
> > >  > 
> >  >>
> > > >  > 
> > >  >  > > >
> > > >
> > > >
> > > > #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 pa

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Douglas N Greve

yes, but remove icoorder

On 03/05/2015 11:50 AM, Matthieu Vanhoutte wrote:
> 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  >:
>
> 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
> 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
> >  
> >
> > >  
> >   > >
> > >
> > >
> > > #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.f

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Matthieu Vanhoutte

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 :

> 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  > >:
> >
> >
> > 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
> > 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

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Douglas N Greve

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  >:
>
>
> 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
> 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
> >  
> >
> > >  
> >   > >
> > >
> > > On 03/02/2015 04:04 AM, Matthieu Vanhoutte wrote:
> > > > Dear Doug,
> > > >
> > > > Thank you for helping !
> > > >
> > > > Yes I directly u

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Matthieu Vanhoutte

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 3mris_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 :

>
> 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  > >:
> >
> >
> >
> > #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
> > 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

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Douglas N Greve


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  >:
>
>
>
> #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
> 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
> >  
> >
> > >  
> >   > >
> > >
> > > 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). Wher

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Matthieu Vanhoutte

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 :

>
>
> #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  > >:
> >
> >
> > 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
> > 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 --

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Douglas N Greve

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 
> 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
> 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
> mailto:gr...@nmr.mgh.harvard.edu>
> >

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Douglas N Greve



#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  >:
>
>
> 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
> 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
> >>

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Matthieu Vanhoutte

*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 3mris_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 :

> 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 3mris_w_to_curv **subj_id lh 
> **lh.fwhm3.cbf.w
> *
>
>
>
>
>
>
>
> *lh.fwhm3.cbfmv ${DIR}/surf/lh.fwhm${FWHM}.intensity
> ${DIR}/ictus/lh.fwhm${FWHM}.intensityrm -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 :
>
>>
>> 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 > > >:
>> >
>> >
>> > 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

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-05 Thread Matthieu Vanhoutte

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 3mris_w_to_curv **subj_id lh
**lh.fwhm3.cbf.w
*







*lh.fwhm3.cbfmv ${DIR}/surf/lh.fwhm${FWHM}.intensity
${DIR}/ictus/lh.fwhm${FWHM}.intensityrm -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 :

>
> 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  > >:
> >
> >
> > 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   Freesurfer@nmr.mgh.harvard.edu>
> >> https://mail

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-02 Thread Douglas N Greve


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  >:
>
>
> 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  
>> 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
>
>
> 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

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-02 Thread Matthieu Vanhoutte

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 ?

2) Smoothing with mris_fwhm is a good way with --mask option ?

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 :

>
> 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 
> listfreesur...@nmr.mgh.harvard.eduhttps://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
>
>
> 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


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.

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-01 Thread Douglas Greve



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
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


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.

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

16 matches

Site Navigation

Mail list logo

Footer information