On Fri, Jan 27, 2017 at 11:15 AM, Douglas N Greve <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 wrote:
>
>
> Sent from my BlackBerry 10 smartphone.
> *From: *miracle ozzoude <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).
> 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>> 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> 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>
> > 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> 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.
> >>>
> >>>
> >>>
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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