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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