On Fri, Jan 27, 2017 at 12:05 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

You would only use that if you wanted the pvf in the FS-specific
"talairach" space. Is that what you want?

On 01/27/2017 12:01 PM, miracle ozzoude wrote:
> Thanks doug for the response. can i use the talairach.lta in the
> transform folder (subjects/mri/transforms/talairach.lta). thanks
> Best,
> Paul
>
> On Fri, Jan 27, 2017 at 11:15 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
>
> The lta would come from registering the volume where you want the PVF
> (eg, fMRI, PET, DTI) to the anatomical. If you want it in the
> anatomical
> space, then use --regheader subjectname instead of --reg. We do not
> compute prob of WM (this is not really a meaningful quantity
> despite the
> use of this term in VBM)
>
>
> On 01/27/2017 09:25 AM, miracooloz@gmail.com
> <mailto:miracooloz@gmail.com> wrote:
> >
> >
> > Sent from my BlackBerry 10 smartphone.
> > *From: *miracle ozzoude <miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>>
> > *Sent: *Thursday, January 26, 2017 7:36 PM
> > *To: *Freesurfer support list
> > *Subject: *Re: [Freesurfer] White matter probability map.
> >
> >
> > hello doug,
> > Thank you.
> > 1) where can i find this lta file? I looked for it in the mri and
> > surface folders but it wasn't there. do i need to run another
> command
> > in order to generate it?
> > 2) Is this the right command? mri_compute_volume_fractions --o pvf
> > --reg filename.lta (location of .lta)
> > 3)Also, Is there a command that converts the results from
> > mri_compute_volume_fractions (which is the volume fraction map) into
> > probability map?
> > 3) I searched the forum and various posts mentioned using
> mri_ca_label
> > to create probablity maps of tissue segmentations (e.g.,
> >
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046425.html
> <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-July/046425.html>).
> > Is this truth? If yes, is it possible to use it with
> > mri_compute_volume_fractions or not?
> > Thank you,
> > Paul.
> >
> > On Thu, Jan 26, 2017 at 6:24 PM, Douglas N Greve
> > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu
> <mailto:greve@nmr.mgh.harvard.edu>>> wrote:
> >
> > Run it something like
> >
> > mri_compute_volume_fractions --o pvf --reg register.dof6.lta
> >
> > where the lta file is a registration file between the FS
> anat and the
> > volume that you want to get the PVFs for. The output will
> have a base
> > name of pvf, eg,
> >
> > pvf.cortex.mgz pvf.csf.mgz pvf.subcort_gm.mgz pvf.wm.mgz
> >
> >
> >
> >
> >
> > On 01/26/2017 06:14 PM, miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>
> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> wrote:
> > > Hello Douglas,
> > > Thank you. When I looked up the command with --help, it said "
> > computes partial volume fractions for cortex, subcortical GM, WM
> > and CSf". What volume do I give the command as an input? T1,
> > orig.mgz ‎.
> > > Best,
> > > Miracle
> > >
> > > Sent from my BlackBerry 10 smartphone.
> > > Original Message
> > > From: Douglas N Greve‎
> > > Sent: Thursday, January 26, 2017 5:54 PM
> > > To: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > Reply To: Freesurfer support list
> > > Subject: Re: [Freesurfer] White matter probability map.
> > >
> > > ps, it is not a probability map per se but the volume fraction
> > (0-1) map
> > >
> > >
> > > On 01/26/2017 05:52 PM, Douglas N Greve wrote:
> > >> Try mri_compute_volume_fractions
> > >>
> > >>
> > >> On 01/26/2017 05:49 PM, miracooloz@gmail.com
> <mailto:miracooloz@gmail.com>
> > <mailto:miracooloz@gmail.com <mailto:miracooloz@gmail.com>> wrote:
> > >>> Hello Freesurfer,
> > >>> Is there a way to extract tissue probability map for
> white matter
> > >>> in FS. Thank you
> > >>> Best,
> > >>> Miracle
> > >>> Sent from my BlackBerry 10 smartphone.
> > >>>
> > >>>
> > >>>
> > >>> _______________________________________________
> > >>> Freesurfer mailing list
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>
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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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