External Email - Use Caution
Hi freesurfer,
I want to do registration on two image volumes nifti file. What are the commands I have to use to do the registration?
Shrabani Ghosh
what kinds of volumes are they and why are you registering them? cheers Bruce On Thu, 20 Jun 2019, Shrabani Ghosh wrote:
External Email - Use Caution
Hi freesurfer, I want to do registration on two image volumes nifti file. What are the commands I have to use to do the registration?
Shrabani Ghosh
External Email - Use Caution
The fixed volume is my model volume and the other is a patient volume (moving )that I want to fit and to the fixed volume. They are different in size and they have to be perfectly aligned. Please guide me on how to do the registration. 8.png is the model volume. 9.png is the patient volume. 10.png is the outline of their size. the smaller one is the moving image and the bigger one is the fixed image.
On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
what kinds of volumes are they and why are you registering them? cheers Bruce On Thu, 20 Jun 2019, Shrabani Ghosh wrote:
External Email - Use CautionHi freesurfer, I want to do registration on two image volumes nifti file. What are the
commands I have to use to do
the registration?
Shrabani Ghosh
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Shrabani
I'm not even sure what these are images of. If you are looking for general-purpose registration tools you can try ANTS or something like that.
cheers Bruce
On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use Caution
The fixed volume is my model volume and the other is a patient volume (moving )that I want to fit and to the fixed volume. They are different in size and they have to be perfectly aligned. Please guide me on how to do the registration. 8.png is the model volume. 9.png is the patient volume. 10.png is the outline of their size. the smaller one is the moving image and the bigger one is the fixed image.
On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: what kinds of volumes are they and why are you registering them? cheers Bruce On Thu, 20 Jun 2019, Shrabani Ghosh wrote:
> > External Email - Use Caution > > Hi freesurfer, > I want to do registration on two image volumes nifti file. What are the commands I have to use to do > the registration? > > Shrabani Ghosh > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
These are skull images of axial representation. Can't I use freesurfer? Because here interpolation is important.
On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shrabani
I'm not even sure what these are images of. If you are looking for general-purpose registration tools you can try ANTS or something like that.
cheers Bruce
On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use CautionThe fixed volume is my model volume and the other is a patient volume
(moving )that I want to fit
and to the fixed volume. They are different in size and they have to be
perfectly aligned. Please
guide me on how to do the registration. 8.png is the model volume. 9.png is the patient volume. 10.png is the outline of their size. the smaller one is the moving image
and the bigger one is the
fixed image.
On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
what kinds of volumes are they and why are you registering them? cheers Bruce On Thu, 20 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > Hi freesurfer, > I want to do registration on two image volumes nifti file. Whatare the commands I
have to use to do > the registration? > > Shrabani Ghosh > >_______________________________________________ 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
not unless you also have an image of the whole brain. Even then I'm not sure it will do what you want, although I'm still not clear on exactly what you are doing. Registering one image of the skull to a model? Why?
On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use Caution
These are skull images of axial representation. Can't I use freesurfer? Because here interpolation is important.
On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Shrabani
I'm not even sure what these are images of. If you are looking for general-purpose registration tools you can try ANTS or something like that. cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > The fixed volume is my model volume and the other is a patient volume (moving )that I want to fit > and to the fixed volume. They are different in size and they have to be perfectly aligned. Please > guide me on how to do the registration. 8.png is the model volume. > 9.png is the patient volume. > 10.png is the outline of their size. the smaller one is the moving image and the bigger one is the > fixed image. > > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > what kinds of volumes are they and why are you registering them? > cheers > Bruce > On Thu, 20 > Jun 2019, Shrabani Ghosh wrote: > > > > > External Email - Use Caution > > > > Hi freesurfer, > > I want to do registration on two image volumes nifti file. What are the commands I > have to use to do > > the registration? > > > > Shrabani Ghosh > > > >_______________________________________________ > 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
External Email - Use Caution
So, you mean to say that two volumes need to be exactly same kind and having same information? So I have generated a skull foramina model(which is triangular mesh) from the fixed image volume. Now I want to register the model with a general patient data volume. But mesh and volume cannot be registered so that I am trying to register the two volumes so that the model will warp on to the patient data perfectly.
regards Shrabani Ghosh
On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
not unless you also have an image of the whole brain. Even then I'm not sure it will do what you want, although I'm still not clear on exactly what you are doing. Registering one image of the skull to a model? Why?
On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use CautionThese are skull images of axial representation. Can't I use freesurfer?
Because here interpolation
is important.
On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
Hi Shrabani I'm not even sure what these are images of. If you are looking for general-purpose registration tools you can try ANTS or somethinglike that.
cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > The fixed volume is my model volume and the other is a patientvolume (moving )that I
want to fit > and to the fixed volume. They are different in size and theyhave to be perfectly
aligned. Please > guide me on how to do the registration. 8.png is the modelvolume.
> 9.png is the patient volume. > 10.png is the outline of their size. the smaller one is themoving image and the
bigger one is the > fixed image. > > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> what kinds of volumes are they and why are you registeringthem?
> cheers > Bruce > On Thu, 20 > Jun 2019, Shrabani Ghosh wrote: > > > > > External Email - Use Caution > > > > Hi freesurfer, > > I want to do registration on two image volumes niftifile. What are the
commands I > have to use to do > > the registration? > > > > Shrabani Ghosh > > > >_______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Shrabani
no, that's not really what I'm saying. In any case, I'm not sure FreeSurfer is the right tool for you to use for this.
cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use Caution
So, you mean to say that two volumes need to be exactly same kind and having same information? So I have generated a skull foramina model(which is triangular mesh) from the fixed image volume. Now I want to register the model with a general patient data volume. But mesh and volume cannot be registered so that I am trying to register the two volumes so that the model will warp on to the patient data perfectly.
regards Shrabani Ghosh
On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: not unless you also have an image of the whole brain. Even then I'm not sure it will do what you want, although I'm still not clear on exactly what you are doing. Registering one image of the skull to a model? Why?
On Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > These are skull images of axial representation. Can't I use freesurfer? Because here interpolation > is important. > > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Shrabani > > I'm not even sure what these are images of. If you are looking for > general-purpose registration tools you can try ANTS or something like that. > > cheers > Bruce > > > On Fri, 21 Jun 2019, Shrabani > Ghosh wrote: > > > > > External Email - Use Caution > > > > The fixed volume is my model volume and the other is a patient volume (moving )that I > want to fit > > and to the fixed volume. They are different in size and they have to be perfectly > aligned. Please > > guide me on how to do the registration. 8.png is the model volume. > > 9.png is the patient volume. > > 10.png is the outline of their size. the smaller one is the moving image and the > bigger one is the > > fixed image. > > > > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > what kinds of volumes are they and why are you registering them? > > cheers > > Bruce > > On Thu, 20 > > Jun 2019, Shrabani Ghosh wrote: > > > > > > > > External Email - Use Caution > > > > > > Hi freesurfer, > > > I want to do registration on two image volumes nifti file. What are the > commands I > > have to use to do > > > the registration? > > > > > > Shrabani Ghosh > > > > > >_______________________________________________ > > 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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
So in which case, freesurfer is applicable. Because I got a suggestion for CT to CT registration, I can use freesurfer.
Thanks
On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shrabani
no, that's not really what I'm saying. In any case, I'm not sure FreeSurfer is the right tool for you to use for this.
cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use CautionSo, you mean to say that two volumes need to be exactly same kind and
having same information? So I
have generated a skull foramina model(which is triangular mesh) from the
fixed image volume. Now I
want to register the model with a general patient data volume. But mesh
and volume cannot be
registered so that I am trying to register the two volumes so that the
model will warp on to the
patient data perfectly.
regards Shrabani Ghosh
On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
not unless you also have an image of the whole brain. Even thenI'm not
sure it will do what you want, although I'm still not clear onexactly what
you are doing. Registering one image of the skull to a model? Why? On Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > These are skull images of axial representation. Can't I usefreesurfer? Because here
interpolation > is important. > > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> Hi Shrabani > > I'm not even sure what these are images of. If you arelooking for
> general-purpose registration tools you can try ANTS orsomething like that.
> > cheers > Bruce > > > On Fri, 21 Jun 2019, Shrabani > Ghosh wrote: > > > > > External Email - Use Caution > > > > The fixed volume is my model volume and the other is apatient volume (moving
)that I > want to fit > > and to the fixed volume. They are different in size andthey have to be
perfectly > aligned. Please > > guide me on how to do the registration. 8.png is themodel volume.
> > 9.png is the patient volume. > > 10.png is the outline of their size. the smaller one isthe moving image and
the > bigger one is the > > fixed image. > > > > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote: > > what kinds of volumes are they and why are youregistering them?
> > cheers > > Bruce > > On Thu, 20 > > Jun 2019, Shrabani Ghosh wrote: > > > > > > > > External Email - Use Caution > > > > > > Hi freesurfer, > > > I want to do registration on two image volumesnifti file. What are
the > commands I > > have to use to do > > > the registration? > > > > > > Shrabani Ghosh > > > > > >_______________________________________________ > > 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
> > >_______________________________________________ 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
Hi Shrabani
you can read about FS on our wiki. We generally require a T1-weighted MRI as input and build models of lots of things from it (including skull, which will be more accurate if you also have a PD or T2-weighted image).
cheers Bruce
On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use Caution
So in which case, freesurfer is applicable. Because I got a suggestion for CT to CT registration, I can use freesurfer. Thanks
On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Shrabani
no, that's not really what I'm saying. In any case, I'm not sure FreeSurfer is the right tool for you to use for this. cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > So, you mean to say that two volumes need to be exactly same kind and having same information? So I > have generated a skull foramina model(which is triangular mesh) from the fixed image volume. Now I > want to register the model with a general patient data volume. But mesh and volume cannot be > registered so that I am trying to register the two volumes so that the model will warp on to the > patient data perfectly. > > regards > Shrabani Ghosh > > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > not unless you also have an image of the whole brain. Even then I'm not > sure it will do what you want, although I'm still not clear on exactly what > you are doing. Registering one image of the skull to a model? Why? > > On Fri, 21 Jun > 2019, Shrabani Ghosh wrote: > > > > > External Email - Use Caution > > > > These are skull images of axial representation. Can't I use freesurfer? Because here > interpolation > > is important. > > > > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > Hi Shrabani > > > > I'm not even sure what these are images of. If you are looking for > > general-purpose registration tools you can try ANTS or something like that. > > > > cheers > > Bruce > > > > > > On Fri, 21 Jun 2019, Shrabani > > Ghosh wrote: > > > > > > > > External Email - Use Caution > > > > > > The fixed volume is my model volume and the other is a patient volume (moving > )that I > > want to fit > > > and to the fixed volume. They are different in size and they have to be > perfectly > > aligned. Please > > > guide me on how to do the registration. 8.png is the model volume. > > > 9.png is the patient volume. > > > 10.png is the outline of their size. the smaller one is the moving image and > the > > bigger one is the > > > fixed image. > > > > > > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> > wrote: > > > what kinds of volumes are they and why are you registering them? > > > cheers > > > Bruce > > > On Thu, 20 > > > Jun 2019, Shrabani Ghosh wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > Hi freesurfer, > > > > I want to do registration on two image volumes nifti file. What are > the > > commands I > > > have to use to do > > > > the registration? > > > > > > > > Shrabani Ghosh > > > > > > > >_______________________________________________ > > > 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 > > > > > >_______________________________________________ > 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
External Email - Use Caution
Okay Thank You for your all the responses.
On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shrabani
you can read about FS on our wiki. We generally require a T1-weighted MRI as input and build models of lots of things from it (including skull, which will be more accurate if you also have a PD or T2-weighted image).
cheers Bruce
On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use CautionSo in which case, freesurfer is applicable. Because I got a suggestion
for CT to CT registration, I
can use freesurfer. Thanks
On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
Hi Shrabani no, that's not really what I'm saying. In any case, I'm not sure FreeSurfer is the right tool for you to use for this. cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > So, you mean to say that two volumes need to be exactly samekind and having same
information? So I > have generated a skull foramina model(which is triangular mesh)from the fixed image
volume. Now I > want to register the model with a general patient data volume.But mesh and volume
cannot be > registered so that I am trying to register the two volumes sothat the model will warp
on to the > patient data perfectly. > > regards > Shrabani Ghosh > > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> not unless you also have an image of the whole brain. Eventhen I'm not
> sure it will do what you want, although I'm still notclear on exactly what
> you are doing. Registering one image of the skull to amodel? Why?
> > On Fri, 21 Jun > 2019, Shrabani Ghosh wrote: > > > > > External Email - Use Caution > > > > These are skull images of axial representation. Can't Iuse freesurfer?
Because here > interpolation > > is important. > > > > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote: > > Hi Shrabani > > > > I'm not even sure what these are images of. If youare looking for
> > general-purpose registration tools you can tryANTS or something like
that. > > > > cheers > > Bruce > > > > > > On Fri, 21 Jun 2019, Shrabani > > Ghosh wrote: > > > > > > > > External Email - Use Caution > > > > > > The fixed volume is my model volume and theother is a patient volume
(moving > )that I > > want to fit > > > and to the fixed volume. They are different insize and they have to
be > perfectly > > aligned. Please > > > guide me on how to do the registration. 8.png isthe model volume.
> > > 9.png is the patient volume. > > > 10.png is the outline of their size. the smallerone is the moving
image and > the > > bigger one is the > > > fixed image. > > > > > > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> > wrote: > > > what kinds of volumes are they and why areyou registering them?
> > > cheers > > > Bruce > > > On Thu, 20 > > > Jun 2019, Shrabani Ghosh wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > Hi freesurfer, > > > > I want to do registration on two imagevolumes nifti file.
What are > the > > commands I > > > have to use to do > > > > the registration? > > > > > > > > Shrabani Ghosh > > > > > > >
> > > 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
> > > > > >_______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
I am using elastix. And I think it does something similar like ANTS. Do you think I should get the proper output using elastix?
On Fri, Jun 21, 2019 at 1:01 PM Shrabani Ghosh srbn.ghosh99@gmail.com wrote:
Okay Thank You for your all the responses.
On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shrabani
you can read about FS on our wiki. We generally require a T1-weighted MRI as input and build models of lots of things from it (including skull, which will be more accurate if you also have a PD or T2-weighted image).
cheers Bruce
On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use CautionSo in which case, freesurfer is applicable. Because I got a suggestion
for CT to CT registration, I
can use freesurfer. Thanks
On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
Hi Shrabani no, that's not really what I'm saying. In any case, I'm not sure FreeSurfer is the right tool for you to use for this. cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > So, you mean to say that two volumes need to be exactly samekind and having same
information? So I > have generated a skull foramina model(which is triangular mesh)from the fixed image
volume. Now I > want to register the model with a general patient data volume.But mesh and volume
cannot be > registered so that I am trying to register the two volumes sothat the model will warp
on to the > patient data perfectly. > > regards > Shrabani Ghosh > > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> not unless you also have an image of the whole brain.Even then I'm not
> sure it will do what you want, although I'm still notclear on exactly what
> you are doing. Registering one image of the skull to amodel? Why?
> > On Fri, 21 Jun > 2019, Shrabani Ghosh wrote: > > > > > External Email - Use Caution > > > > These are skull images of axial representation. Can't Iuse freesurfer?
Because here > interpolation > > is important. > > > > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote: > > Hi Shrabani > > > > I'm not even sure what these are images of. Ifyou are looking for
> > general-purpose registration tools you can tryANTS or something like
that. > > > > cheers > > Bruce > > > > > > On Fri, 21 Jun 2019, Shrabani > > Ghosh wrote: > > > > > > > > External Email - Use Caution > > > > > > The fixed volume is my model volume and theother is a patient volume
(moving > )that I > > want to fit > > > and to the fixed volume. They are different insize and they have to
be > perfectly > > aligned. Please > > > guide me on how to do the registration. 8.pngis the model volume.
> > > 9.png is the patient volume. > > > 10.png is the outline of their size. thesmaller one is the moving
image and > the > > bigger one is the > > > fixed image. > > > > > > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> > wrote: > > > what kinds of volumes are they and whyare you registering them?
> > > cheers > > > Bruce > > > On Thu, 20 > > > Jun 2019, Shrabani Ghosh wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > Hi freesurfer, > > > > I want to do registration on two imagevolumes nifti file.
What are > the > > commands I > > > have to use to do > > > > the registration? > > > > > > > > Shrabani Ghosh > > > > > > >
> > > 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
> > > > > >_______________________________________________ > 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Shrabani
I really don't know - I don't have any experience registering skulls. sorry Bruce
On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use Caution
I am using elastix. And I think it does something similar like ANTS. Do you think I should get the proper output using elastix?
On Fri, Jun 21, 2019 at 1:01 PM Shrabani Ghosh srbn.ghosh99@gmail.com wrote: Okay Thank You for your all the responses.
On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Shrabani
you can read about FS on our wiki. We generally require a T1-weighted MRI as input and build models of lots of things from it (including skull, which will be more accurate if you also have a PD or T2-weighted image). cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > So in which case, freesurfer is applicable. Because I got a suggestion for CT to CT registration, I > can use freesurfer. > Thanks > > On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > Hi Shrabani > > no, that's not really what I'm saying. In any case, I'm not sure > FreeSurfer is the right tool for you to use for this. > > cheers > Bruce > On Fri, 21 Jun 2019, > Shrabani Ghosh wrote: > > > > > External Email - Use Caution > > > > So, you mean to say that two volumes need to be exactly same kind and having same > information? So I > > have generated a skull foramina model(which is triangular mesh) from the fixed image > volume. Now I > > want to register the model with a general patient data volume. But mesh and volume > cannot be > > registered so that I am trying to register the two volumes so that the model will warp > on to the > > patient data perfectly. > > > > regards > > Shrabani Ghosh > > > > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > not unless you also have an image of the whole brain. Even then I'm not > > sure it will do what you want, although I'm still not clear on exactly what > > you are doing. Registering one image of the skull to a model? Why? > > > > On Fri, 21 Jun > > 2019, Shrabani Ghosh wrote: > > > > > > > > External Email - Use Caution > > > > > > These are skull images of axial representation. Can't I use freesurfer? > Because here > > interpolation > > > is important. > > > > > > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> > wrote: > > > Hi Shrabani > > > > > > I'm not even sure what these are images of. If you are looking for > > > general-purpose registration tools you can try ANTS or something like > that. > > > > > > cheers > > > Bruce > > > > > > > > > On Fri, 21 Jun 2019, Shrabani > > > Ghosh wrote: > > > > > > > > > > > External Email - Use Caution > > > > > > > > The fixed volume is my model volume and the other is a patient volume > (moving > > )that I > > > want to fit > > > > and to the fixed volume. They are different in size and they have to > be > > perfectly > > > aligned. Please > > > > guide me on how to do the registration. 8.png is the model volume. > > > > 9.png is the patient volume. > > > > 10.png is the outline of their size. the smaller one is the moving > image and > > the > > > bigger one is the > > > > fixed image. > > > > > > > > On Fri, Jun 21, 2019 at 10:22 AM Bruce Fischl > <fischl@nmr.mgh.harvard.edu> > > wrote: > > > > what kinds of volumes are they and why are you registering them? > > > > cheers > > > > Bruce > > > > On Thu, 20 > > > > Jun 2019, Shrabani Ghosh wrote: > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > Hi freesurfer, > > > > > I want to do registration on two image volumes nifti file. > What are > > the > > > commands I > > > > have to use to do > > > > > the registration? > > > > > > > > > > Shrabani Ghosh > > > > > > > > > >_______________________________________________ > > > > 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 > > > > > > > > >_______________________________________________ > > 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 > > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Okay, thank you.
On Fri, Jun 21, 2019 at 2:24 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Shrabani
I really don't know - I don't have any experience registering skulls. sorry Bruce
On Fri, 21 Jun 2019, Shrabani Ghosh wrote:
External Email - Use CautionI am using elastix. And I think it does something similar like ANTS. Do
you think I should get the
proper output using elastix?
On Fri, Jun 21, 2019 at 1:01 PM Shrabani Ghosh srbn.ghosh99@gmail.com
wrote:
Okay Thank You for your all the responses.On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl <
fischl@nmr.mgh.harvard.edu> wrote:
Hi Shrabani you can read about FS on our wiki. We generally require aT1-weighted MRI
as input and build models of lots of things from it (includingskull, which
will be more accurate if you also have a PD or T2-weighted image). cheers Bruce On Fri, 21 Jun 2019, Shrabani Ghosh wrote: > > External Email - Use Caution > > So in which case, freesurfer is applicable. Because I got asuggestion for CT to
CT registration, I > can use freesurfer. > Thanks > > On Fri, Jun 21, 2019 at 12:42 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote: > Hi Shrabani > > no, that's not really what I'm saying. In any case, I'mnot sure
> FreeSurfer is the right tool for you to use for this. > > cheers > Bruce > On Fri, 21 Jun 2019, > Shrabani Ghosh wrote: > > > > > External Email - Use Caution > > > > So, you mean to say that two volumes need to be exactlysame kind and
having same > information? So I > > have generated a skull foramina model(which istriangular mesh) from the
fixed image > volume. Now I > > want to register the model with a general patient datavolume. But mesh
and volume > cannot be > > registered so that I am trying to register the twovolumes so that the
model will warp > on to the > > patient data perfectly. > > > > regards > > Shrabani Ghosh > > > > On Fri, Jun 21, 2019 at 12:06 PM Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: > > not unless you also have an image of the wholebrain. Even then
I'm not > > sure it will do what you want, although I'm stillnot clear on
exactly what > > you are doing. Registering one image of the skullto a model? Why?
> > > > On Fri, 21 Jun > > 2019, Shrabani Ghosh wrote: > > > > > > > > External Email - Use Caution > > > > > > These are skull images of axial representation.Can't I use
freesurfer? > Because here > > interpolation > > > is important. > > > > > > On Fri, Jun 21, 2019 at 11:58 AM Bruce Fischl <fischl@nmr.mgh.harvard.edu> > wrote: > > > Hi Shrabani > > > > > > I'm not even sure what these are imagesof. If you are
looking for > > > general-purpose registration tools you cantry ANTS or
something like > that. > > > > > > cheers > > > Bruce > > > > > > > > > On Fri, 21 Jun 2019, Shrabani > > > Ghosh wrote: > > > > > > > > > > > External Email - UseCaution
> > > > > > > > The fixed volume is my model volume andthe other is a
patient volume > (moving > > )that I > > > want to fit > > > > and to the fixed volume. They aredifferent in size and
they have to > be > > perfectly > > > aligned. Please > > > > guide me on how to do theregistration. 8.png is the
model volume. > > > > 9.png is the patient volume. > > > > 10.png is the outline of their size. thesmaller one is
the moving > image and > > the > > > bigger one is the > > > > fixed image. > > > > > > > > On Fri, Jun 21, 2019 at 10:22 AM BruceFischl
> <fischl@nmr.mgh.harvard.edu> > > wrote: > > > > what kinds of volumes are they andwhy are you
registering them? > > > > cheers > > > > Bruce > > > > On Thu, 20 > > > > Jun 2019, Shrabani Ghosh wrote: > > > > > > > > > > > > > > External Email - UseCaution
> > > > > > > > > > Hi freesurfer, > > > > > I want to do registration on twoimage volumes
nifti file. > What are > > the > > > commands I > > > > have to use to do > > > > > the registration? > > > > > > > > > > Shrabani Ghosh > > > > > > > > >
> > > > 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 > > > > > > > > >_______________________________________________ > > 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
> > >_______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Shrabani Ghosh