Dear Professor Bruce I'm just trying to convert lh.pial surface to the volume with the down below command but the output doesn't make any sense ( lh.voulme contains zero). Could you please help? Mris_volume topo_defect_after/surf/rh.pial
Thank you! On Tue, Sep 19, 2017 at 1:11 PM Fereshte fereshte.ramezani@gmail.com wrote:
On Tue, Sep 19, 2017 at 11:51 AM Fereshte fereshte.ramezani@gmail.com wrote:
I changed the FreeSurfer version to 6 and now i could find it. Thank you! Cheers
On Sat, Sep 16, 2017 at 9:21 PM Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Is it not in $FREESURFER_HOME/bin ? What version are you using?
On 9/16/17 12:05 PM, Fereshte wrote:
Well i did ask if it was possible to obtain the volume of Pial surface and here's the response;
"sure, mris_volume will give you the interior volume of any closed surface using the divergence formula. Note that this is *not* the volume of the ribbon but rather the volume of the entire interior"
I can't see mris_volume in FreeSurfer commands.
On Sat, Sep 16, 2017 at 8:09 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
sorry, can you clarify what your question is?
On Sat, 16 Sep 2017, Fereshte wrote:
Dear FreeSurfer developers I couldn't find the mentioned mris_volume in the commands. Shall i
use mri_vol2surf or something?
Looking forward to hearing from you! On Tue, Sep 5, 2017 at 9:46 AM Fereshte fereshte.ramezani@gmail.com
wrote:
Hi Bruce,Thank you for your replies. Cheers
On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
Hi Fereshte the algorithm is documented in the recon1 1999 NeuroImage and2000 PNAS
papers cheers Bruce On Mon, 4 Sep 2017, Fereshte wrote: > What's the algorithm used to expand inner cortical boundary (to achieve the
outer cortical boundary > in pial surface) in FreeSurfer? > On Mon, Sep 4, 2017 at 9:58 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> it will give the interior volume of whatever surfaceyou give it as a
> command line argument. > > On Mon, 4 Sep 2017, Fereshte > wrote: > > > Using the Pial surface; Does it mean mris_volume willgive the inner
cortical boundary > of the > > surface and not the outer boundary? > > Sincerely, > > Fereshte Ramezani > > On Mon, Sep 4, 2017 at 9:53 PM Fereshte <fereshte.ramezani@gmail.com>
wrote: > > > > On Mon, Sep 4, 2017 at 6:46 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > sure, mris_volume will give you the interiorvolume of any closed
surface > > using the divergence formula. Note that this is*not* the volume
of the > > ribbon but rather the volume of the entireinterior
> > > > cheers > > Bruce > > > > > > On Mon, 4 Sep 2017, Fereshte wrote: > > > > > Hello FreeSurfer developersIs it possible tohave the volume of
pial surface > in > > FreeSurfer? > > > > > >_______________________________________________ > > 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 onlyfor the person to
whom it is > > addressed. If you believe this e-mail was sentto you in error and
the e-mail > > contains patient information, please contactthe Partners
Compliance HelpLine at > > http://www.partners.org/complianceline . Ifthe 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
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HelpLine at > http://www.partners.org/complianceline . If the e-mailwas sent to you in
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Hi Fereshte
mris_volumes computes and prints the volume of the interior of a closed surface (a single number). It does not fill the interior. For that, use mris_fill
cheers Bruce On Tue, 19 Sep 2017, Fereshte wrote:
Dear Professor Bruce I'm just trying to convert lh.pial surface to the volume with the down below command but the output doesn't make any sense ( lh.voulme contains zero). Could you please help? Mris_volume topo_defect_after/surf/rh.pial Thank you! On Tue, Sep 19, 2017 at 1:11 PM Fereshte fereshte.ramezani@gmail.com wrote:
On Tue, Sep 19, 2017 at 11:51 AM Fereshte <fereshte.ramezani@gmail.com> wrote: I changed the FreeSurfer version to 6 and now i could find it.Thank you! Cheers
On Sat, Sep 16, 2017 at 9:21 PM Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Is it not in $FREESURFER_HOME/bin ? What version are you using?On 9/16/17 12:05 PM, Fereshte wrote: Well i did ask if it was possible to obtain the volume of Pial surface and here's the response;
"sure, mris_volume will give you the interior volume of any closed surface using the divergence formula. Note that this is *not* the volume of the ribbon but rather the volume of the entire interior"
I can't see mris_volume in FreeSurfer commands.
On Sat, Sep 16, 2017 at 8:09 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: sorry, can you clarify what your question is?
On Sat, 16 Sep 2017, Fereshte wrote: > Dear FreeSurfer developers > I couldn't find the mentioned mris_volume in the commands. Shall i use mri_vol2surf or something? > Looking forward to hearing from you! > On Tue, Sep 5, 2017 at 9:46 AM Fereshte <fereshte.ramezani@gmail.com> wrote: > Hi Bruce, > Thank you for your replies. > Cheers > > On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Fereshte > > the algorithm is documented in the recon1 1999 NeuroImage and 2000 PNAS > papers > > cheers > Bruce > On Mon, 4 Sep 2017, Fereshte wrote: > > > What's the algorithm used to expand inner cortical boundary ( to achieve the > outer cortical boundary > > in pial surface) in FreeSurfer? > > On Mon, Sep 4, 2017 at 9:58 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > it will give the interior volume of whatever surface you give it as a > > command line argument. > > > > On Mon, 4 Sep 2017, Fereshte > > wrote: > > > > > Using the Pial surface; Does it mean mris_volume will give the inner > cortical boundary > > of the > > > surface and not the outer boundary? > > > Sincerely, > > > Fereshte Ramezani > > > On Mon, Sep 4, 2017 at 9:53 PM Fereshte <fereshte.ramezani@gmail.com> > wrote: > > > > > > On Mon, Sep 4, 2017 at 6:46 PM Bruce Fischl > <fischl@nmr.mgh.harvard.edu> wrote: > > > sure, mris_volume will give you the interior volume of any closed > surface > > > using the divergence formula. Note that this is *not* the volume > of the > > > ribbon but rather the volume of the entire interior > > > > > > cheers > > > Bruce > > > > > > > > > On Mon, 4 Sep 2017, Fereshte wrote: > > > > > > > Hello FreeSurfer developersIs it possible to have the volume of > pial surface > > in > > > FreeSurfer? > > > > > > > >_______________________________________________ > > > 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. > > > > > > > > >_______________________________________________ > > 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. > > > > > >_______________________________________________ > 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. > > >_______________________________________________ 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.
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Does it give the exact volume ( the volume which the surface was made from) or it gives an approximation of the volume? ( the toolboxes I've already worked with for such a purpose; give poor approximations). Thank you!
On Tue, Sep 19, 2017 at 6:40 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Fereshte
mris_volumes computes and prints the volume of the interior of a closed surface (a single number). It does not fill the interior. For that, use mris_fill
cheers Bruce On Tue, 19 Sep 2017, Fereshte wrote:
Dear Professor Bruce I'm just trying to convert lh.pial surface to the volume with the down
below command but the output
doesn't make any sense ( lh.voulme contains zero). Could you please
help?
Mris_volume topo_defect_after/surf/rh.pial
Thank you! On Tue, Sep 19, 2017 at 1:11 PM Fereshte fereshte.ramezani@gmail.com
wrote:
On Tue, Sep 19, 2017 at 11:51 AM Fereshte <fereshte.ramezani@gmail.com> wrote:
I changed the FreeSurfer version to 6 and now i could find it.Thank you! Cheers
On Sat, Sep 16, 2017 at 9:21 PM Douglas Greve greve@nmr.mgh.harvard.edu
wrote:
Is it not in $FREESURFER_HOME/bin ? What version are you using?On 9/16/17 12:05 PM, Fereshte wrote: Well i did ask if it was possible to obtain the volume of Pial
surface
and here's the response;"sure, mris_volume will give you the interior volume of any closed
surface
using the divergence formula. Note that this is *not* the volume of the ribbon but rather the volume of the entire interior"
I can't see mris_volume in FreeSurfer commands.
On Sat, Sep 16, 2017 at 8:09 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: sorry, can you clarify what your question is?
On Sat, 16 Sep 2017, Fereshte wrote: > Dear FreeSurfer developers > I couldn't find the mentioned mris_volume in the commands. Shall i use mri_vol2surf or something? > Looking forward to hearing from you! > On Tue, Sep 5, 2017 at 9:46 AM Fereshte <fereshte.ramezani@gmail.com> wrote: > Hi Bruce, > Thank you for your replies. > Cheers > > On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Fereshte > > the algorithm is documented in the recon1 1999 NeuroImage and 2000 PNAS > papers > > cheers > Bruce > On Mon, 4 Sep 2017, Fereshte wrote: > > > What's the algorithm used to expand inner cortical boundary ( to achieve the > outer cortical boundary > > in pial surface) in FreeSurfer? > > On Mon, Sep 4, 2017 at 9:58 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > it will give the interior volume of whatever surface you give it as a > > command line argument. > > > > On Mon, 4 Sep 2017, Fereshte > > wrote: > > > > > Using the Pial surface; Does it mean mris_volume will give the inner > cortical boundary > > of the > > > surface and not the outer boundary? > > > Sincerely, > > > Fereshte Ramezani > > > On Mon, Sep 4, 2017 at 9:53 PM Fereshte <fereshte.ramezani@gmail.com> > wrote: > > > > > > On Mon, Sep 4, 2017 at 6:46 PM Bruce Fischl > <fischl@nmr.mgh.harvard.edu> wrote: > > > sure, mris_volume will give you the interior volume of any closed > surface > > > using the divergence formula. Note that this is *not* the volume > of the > > > ribbon but rather the volume of the entire interior > > > > > > cheers > > > Bruce > > > > > > > > > On Mon, 4 Sep 2017, Fereshte wrote: > > > > > > > Hello FreeSurfer developersIs it possible to have the volume of > pial surface > > in > > > FreeSurfer? > > > > > > > >_______________________________________________ > > > 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. > > > > > > > > >_______________________________________________ > > 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. > > > > > >_______________________________________________ > 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. > > >_______________________________________________ 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.
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it should be exact On Wed, 20 Sep 2017, Fereshte wrote:
Does it give the exact volume ( the volume which the surface was made from) or it gives an approximation of the volume? ( the toolboxes I've already worked with for such a purpose; give poor approximations). Thank you!
On Tue, Sep 19, 2017 at 6:40 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Fereshte
mris_volumes computes and prints the volume of the interior of a closed surface (a single number). It does not fill the interior. For that, use mris_fill cheers Bruce On Tue, 19 Sep 2017, Fereshte wrote: > Dear Professor Bruce > I'm just trying to convert lh.pial surface to the volume with the down below command but the output > doesn't make any sense ( lh.voulme contains zero). Could you please help? > Mris_volume topo_defect_after/surf/rh.pial > > Thank you! > On Tue, Sep 19, 2017 at 1:11 PM Fereshte <fereshte.ramezani@gmail.com> wrote: > > On Tue, Sep 19, 2017 at 11:51 AM Fereshte <fereshte.ramezani@gmail.com> wrote: > I changed the FreeSurfer version to 6 and now i could find it. > Thank you! > Cheers > > On Sat, Sep 16, 2017 at 9:21 PM Douglas Greve <greve@nmr.mgh.harvard.edu> wrote: > > Is it not in $FREESURFER_HOME/bin ? What version are you using? > > > On 9/16/17 12:05 PM, Fereshte wrote: > Well i did ask if it was possible to obtain the volume of Pial surface > and here's the response; > > "sure, mris_volume will give you the interior volume of any closed surface > using the divergence formula. Note that this is *not* the volume of the > ribbon but rather the volume of the entire interior" > > I can't see mris_volume in FreeSurfer commands. > > On Sat, Sep 16, 2017 at 8:09 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> > wrote: > sorry, can you clarify what your question is? > > On Sat, 16 Sep 2017, Fereshte > wrote: > > > Dear FreeSurfer developers > > I couldn't find the mentioned mris_volume in the commands. > Shall i use mri_vol2surf or something? > > Looking forward to hearing from you! > > On Tue, Sep 5, 2017 at 9:46 AM Fereshte > <fereshte.ramezani@gmail.com> wrote: > > Hi Bruce, > > Thank you for your replies. > > Cheers > > > > On Tue, Sep 5, 2017 at 4:52 AM Bruce Fischl > <fischl@nmr.mgh.harvard.edu> wrote: > > Hi Fereshte > > > > the algorithm is documented in the recon1 1999 > NeuroImage and 2000 PNAS > > papers > > > > cheers > > Bruce > > On Mon, 4 Sep 2017, Fereshte wrote: > > > > > What's the algorithm used to expand inner cortical > boundary ( to achieve the > > outer cortical boundary > > > in pial surface) in FreeSurfer? > > > On Mon, Sep 4, 2017 at 9:58 PM Bruce Fischl > <fischl@nmr.mgh.harvard.edu> wrote: > > > it will give the interior volume of whatever > surface you give it as a > > > command line argument. > > > > > > On Mon, 4 Sep 2017, Fereshte > > > wrote: > > > > > > > Using the Pial surface; Does it mean > mris_volume will give the inner > > cortical boundary > > > of the > > > > surface and not the outer boundary? > > > > Sincerely, > > > > Fereshte Ramezani > > > > On Mon, Sep 4, 2017 at 9:53 PM Fereshte > <fereshte.ramezani@gmail.com> > > wrote: > > > > > > > > On Mon, Sep 4, 2017 at 6:46 PM Bruce > Fischl > > <fischl@nmr.mgh.harvard.edu> wrote: > > > > sure, mris_volume will give you the > interior volume of any closed > > surface > > > > using the divergence formula. Note that > this is *not* the volume > > of the > > > > ribbon but rather the volume of the > entire interior > > > > > > > > cheers > > > > Bruce > > > > > > > > > > > > On Mon, 4 Sep 2017, Fereshte wrote: > > > > > > > > > Hello FreeSurfer developersIs it > possible to have the volume of > > pial surface > > > in > > > > FreeSurfer? > > > > > > > > > > >_______________________________________________ > > > > 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. > > > > > > > > > > > >_______________________________________________ > > > 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. > > > > > > > > >_______________________________________________ > > 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. > > > > > >_______________________________________________ > 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. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > 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. > > >_______________________________________________ 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.
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