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> 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 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
> 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 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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>>> Freesurfer@nmr.mgh.harvard.edu
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MGH-NMR Center
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