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, miracoo...@gmail.com wrote: > > > Sent from my BlackBerry 10 smartphone. > *From: *miracle ozzoude <miracoo...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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, miracoo...@gmail.com > <mailto:miracoo...@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, miracoo...@gmail.com > <mailto:miracoo...@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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
