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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
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 greve@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
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 . 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.
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
Thanks doug for the response. can i use the talairach.lta in the transform folder (subjects/mri/transforms/talairach.lta). thanks Best, Paul
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.
- 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
-- 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 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
You would only use that if you wanted the pvf in the FS-specific "talairach" space. Is that what you want?
On 01/27/2017 12:01 PM, miracle ozzoude wrote:
Thanks doug for the response. can i use the talairach.lta in the transform folder (subjects/mri/transforms/talairach.lta). thanks Best, Paul
On Fri, Jan 27, 2017 at 11:15 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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 <mailto:miracooloz@gmail.com> wrote: > > > Sent from my BlackBerry 10 smartphone. > *From: *miracle ozzoude <miracooloz@gmail.com <mailto: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 <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> <mailto: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> > <mailto: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> > <mailto: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> > <mailto: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> > <mailto: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> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <mailto: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> > <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> > <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 <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>
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no, I want it in the subject's anatomical space. You suggested i use (mri_compute_volume_fractions --o pvf --regheader subjectname ). However, when i use the command i received an error "--regheader flag needs 2 arguments". What other flag should I specify? Thanks. Best, Paul.
On Fri, Jan 27, 2017 at 12:05 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
You would only use that if you wanted the pvf in the FS-specific "talairach" space. Is that what you want?
On 01/27/2017 12:01 PM, miracle ozzoude wrote:
Thanks doug for the response. can i use the talairach.lta in the transform folder (subjects/mri/transforms/talairach.lta). thanks Best, Paul
On Fri, Jan 27, 2017 at 11:15 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto: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 <mailto:miracooloz@gmail.com> wrote: > > > Sent from my BlackBerry 10 smartphone. > *From: *miracle ozzoude <miracooloz@gmail.com <mailto: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
<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> <mailto: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> > <mailto: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> > <mailto: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 volumefraction
> (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> > <mailto: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> > <mailto: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> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <mailto: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> > <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> > <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 <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>
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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 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/
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Douglas N Greve -
miracle ozzoude -
miracooloz＠gmail.com