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.
- 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. >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- 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> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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