Re: [Freesurfer] Registration of image volumes
External Email - Use Caution Okay, thank you. On Fri, Jun 21, 2019 at 2:24 PM Bruce Fischl 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 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 > wrote: > > Okay Thank You for your all the responses. > > > > On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl < > fis...@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 < > fis...@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 > >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 > > > > > 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. > > > >
Re: [Freesurfer] Registration of image volumes
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 wrote: Okay Thank You for your all the responses. On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl 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 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 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 > 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 > > > wrote: > > > > what kinds of volumes are they and why are you registering them? > > > > cheers > > >
Re: [Freesurfer] Registration of image volumes
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 wrote: > Okay Thank You for your all the responses. > > On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl > 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 < >> fis...@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 < >> fis...@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 < >> fis...@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 >> > >> > > 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 >>
Re: [Freesurfer] Registration of image volumes
External Email - Use Caution Okay Thank You for your all the responses. On Fri, Jun 21, 2019 at 12:50 PM Bruce Fischl 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 < > fis...@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 < > fis...@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 < > fis...@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 > > > > > 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 > > > > > >
Re: [Freesurfer] Registration of image volumes
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 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 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 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 > 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 > > > > >
Re: [Freesurfer] Registration of image volumes
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 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 < > fis...@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 < > fis...@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 < > fis...@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
Re: [Freesurfer] Registration of image volumes
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 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 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 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
Re: [Freesurfer] Registration of image volumes
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 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 < > fis...@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 < > fis...@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
Re: [Freesurfer] Registration of image volumes
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 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 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
Re: [Freesurfer] Registration of image volumes
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 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 < > fis...@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
Re: [Freesurfer] Registration of image volumes
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 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
Re: [Freesurfer] Registration of image volumes
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
