Converting from DWI to DTI

classic Classic list List threaded Threaded
10 messages Options
Reply | Threaded
Open this post in threaded view
|

Converting from DWI to DTI

shoosh moosh
How do I convert from diffusion weighted image (*.nrrd format) to Diffusion tensor image in slicer?
Thanks


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: Converting from DWI to DTI

Demian Wassermann-2
Hi!

On the Diffusion menu -> Utilities there is one called Diffusion Tensor Estimation.

You can find all the details regarding the process in:

Happy to help
Demian




--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:30 PM, shoosh moosh wrote:

How do I convert from diffusion weighted image (*.nrrd format) to Diffusion tensor image in slicer?
Thanks

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: Converting from DWI to DTI

Dominik Meier
In reply to this post by shoosh moosh
Use the "Diffusion Tensor Estimation" module, under Diffusion / Utilities.

Dominik


On Sep 15, 2010, at 2:30 PM, shoosh moosh wrote:

How do I convert from diffusion weighted image (*.nrrd format) to Diffusion tensor image in slicer?
Thanks


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: Converting from DWI to DTI

shoosh moosh
In reply to this post by Demian Wassermann-2
Great, thanks!
Now how do I convert from a DTI that is in (*.nhdr  & *.raw.gz) format to a DTI that is in *.nii.gz format?
Thanks



Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 15:34:06 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Hi!

On the Diffusion menu -> Utilities there is one called Diffusion Tensor Estimation.

You can find all the details regarding the process in:

Happy to help
Demian




--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:30 PM, shoosh moosh wrote:

How do I convert from diffusion weighted image (*.nrrd format) to Diffusion tensor image in slicer?
Thanks

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: Converting from DWI to DTI

Demian Wassermann-2
Mmmmm

that does not have an easy answer I guess. That export feature is not yet implemented. What tools do you want to interact with?

D

--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:59 PM, shoosh moosh wrote:

Great, thanks!
Now how do I convert from a DTI that is in (*.nhdr  & *.raw.gz) format to a DTI that is in *.nii.gz format?
Thanks



Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 15:34:06 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Hi!

On the Diffusion menu -> Utilities there is one called Diffusion Tensor Estimation.

You can find all the details regarding the process in:

Happy to help
Demian




--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:30 PM, shoosh moosh wrote:

How do I convert from diffusion weighted image (*.nrrd format) to Diffusion tensor image in slicer?
Thanks

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject




_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Converting from DWI to DTI

shoosh moosh

Actually I needed it in that format in order to change its resolution from (1x1x3) to (1x1x1). I found this TVResample module in DTI Toolkit that requires the DTI volume to be in *.nii.gz.
But can Slicer change the resolution without having to resort to that tool? And if it does, does it do the interpolation, or does it simply downsample?
Thanks,


Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 16:00:27 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Mmmmm

that does not have an easy answer I guess. That export feature is not yet implemented. What tools do you want to interact with?

D

--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:59 PM, shoosh moosh wrote:

Great, thanks!
Now how do I convert from a DTI that is in (*.nhdr  & *.raw.gz) format to a DTI that is in *.nii.gz format?
Thanks



Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 15:34:06 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Hi!

On the Diffusion menu -> Utilities there is one called Diffusion Tensor Estimation.

You can find all the details regarding the process in:

Happy to help
Demian




--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:30 PM, shoosh moosh wrote:

How do I convert from diffusion weighted image (*.nrrd format) to Diffusion tensor image in slicer?
Thanks

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject




_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: Converting from DWI to DTI

Kikinis, Ron,M.D.
Resample Scalar/Vector/DWI Volume can upsample the DWI and ResampleDTI
can upsample the DTI in Slicer3.



On 9/15/10 3:13 PM, shoosh moosh wrote:

>
> Actually I needed it in that format in order to change its resolution
> from (1x1x3) to (1x1x1). I found this TVResample module in DTI Toolkit
> that requires the DTI volume to be in *.nii.gz.
> But can Slicer change the resolution without having to resort to that
> tool? And if it does, does it do the interpolation, or does it simply
> downsample?
> Thanks,
>
> ------------------------------------------------------------------------
> Subject: Re: [slicer-users] Converting from DWI to DTI
> From: [hidden email]
> Date: Wed, 15 Sep 2010 16:00:27 -0300
> CC: [hidden email]; [hidden email]
> To: [hidden email]
>
> Mmmmm
>
> that does not have an easy answer I guess. That export feature is not
> yet implemented. What tools do you want to interact with?
>
> D
>
> --
> Demian Wassermann, PhD
> [hidden email] <mailto:[hidden email]>
> LMI / PNL / SPL Labs
> Harvard Medical School
> Brigham and Women's Hospital
> 1249 Boylston, Boston, MA, USA
>
> On Sep 15, 2010, at 3:59 PM, shoosh moosh wrote:
>
>     Great, thanks!
>     Now how do I convert from a DTI that is in (*.nhdr & *.raw.gz)
>     format to a DTI that is in *.nii.gz format?
>     Thanks
>
>
>     ------------------------------------------------------------------------
>     Subject: Re: [slicer-users] Converting from DWI to DTI
>     From: [hidden email] <mailto:[hidden email]>
>     Date: Wed, 15 Sep 2010 15:34:06 -0300
>     CC: [hidden email] <mailto:[hidden email]
>     rvard.edu>; [hidden email]
>     <mailto:[hidden email]>
>     To: [hidden email] <mailto:[hidden email]>
>
>     Hi!
>
>     On the Diffusion menu -> Utilities there is one called Diffusion
>     Tensor Estimation.
>
>     You can find all the details regarding the process in:
>     http://www.slicer.org/slicerWiki/index.php/Modules:DiffusionMRIWelcome-Documentation-3.6
>
>     Happy to help
>     Demian
>
>
>
>
>     --
>     Demian Wassermann, PhD
>     [hidden email] <mailto:[hidden email]>
>     LMI / PNL / SPL Labs
>     Harvard Medical School
>     Brigham and Women's Hospital
>     1249 Boylston, Boston, MA, USA
>
>     On Sep 15, 2010, at 3:30 PM, shoosh moosh wrote:
>
>         How do I convert from diffusion weighted image (*.nrrd format)
>         to Diffusion tensor image in slicer?
>         Thanks
>
>         _______________________________________________
>         slicer-users mailing list
>         [hidden email] <mailto:[hidden email]>
>         http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>         To unsubscribe: send email to
>         [hidden email]
>         <mailto:[hidden email]> with
>         unsubscribe as the subject
>
>
>
>
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject

--
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: Converting from DWI to DTI

Isaiah Norton
In reply to this post by shoosh moosh
There is a module called "Resample DTI Volume" under Diffusion->Utilities with various interpolation types available.

On your original question of .nii.gz format: as far as I know, Slicer does not support writing tensor volumes as Nifti (nii). From a quick look, it seems like the underlying library (ITKNiftiImageIO) supports writing the necessary datatype NIFTI_INTENT_SYMMATRIX --so you could probably do  in tcl/python. Another route would be to reshape the raw file and build a header using fslcreatehd

More generally, if you are doing analysis in another program it will be easier to just converdirectly t nii from the original DICOM images if you have them (uing ie: mri_convert from FreeSurfer, dcm2nii, mricro/n, etc..).

-Isaiah

On 09/15/2010 03:13 PM, shoosh moosh wrote:

Actually I needed it in that format in order to change its resolution from (1x1x3) to (1x1x1). I found this TVResample module in DTI Toolkit that requires the DTI volume to be in *.nii.gz.
But can Slicer change the resolution without having to resort to that tool? And if it does, does it do the interpolation, or does it simply downsample?
Thanks,


Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 16:00:27 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Mmmmm

that does not have an easy answer I guess. That export feature is not yet implemented. What tools do you want to interact with?

D

--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:59 PM, shoosh moosh wrote:

Great, thanks!
Now how do I convert from a DTI that is in (*.nhdr  & *.raw.gz) format to a DTI that is in *.nii.gz format?
Thanks



Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 15:34:06 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Hi!

On the Diffusion menu -> Utilities there is one called Diffusion Tensor Estimation.

You can find all the details regarding the process in:

Happy to help
Demian




--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:30 PM, shoosh moosh wrote:

How do I convert from diffusion weighted image (*.nrrd format) to Diffusion tensor image in slicer?
Thanks

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject



_______________________________________________ slicer-users mailing list [hidden email] http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: Converting from DWI to DTI

shoosh moosh
Does the Resample DTI Volume module do the interpolation Log-Euclidean?
Thanks


Date: Wed, 15 Sep 2010 15:49:36 -0400
From: [hidden email]
To: [hidden email]
Subject: Re: [slicer-users] Converting from DWI to DTI

There is a module called "Resample DTI Volume" under Diffusion->Utilities with various interpolation types available.

On your original question of .nii.gz format: as far as I know, Slicer does not support writing tensor volumes as Nifti (nii). From a quick look, it seems like the underlying library (ITKNiftiImageIO) supports writing the necessary datatype NIFTI_INTENT_SYMMATRIX --so you could probably do  in tcl/python. Another route would be to reshape the raw file and build a header using fslcreatehd

More generally, if you are doing analysis in another program it will be easier to just converdirectly t nii from the original DICOM images if you have them (uing ie: mri_convert from FreeSurfer, dcm2nii, mricro/n, etc..).

-Isaiah

On 09/15/2010 03:13 PM, shoosh moosh wrote:

Actually I needed it in that format in order to change its resolution from (1x1x3) to (1x1x1). I found this TVResample module in DTI Toolkit that requires the DTI volume to be in *.nii.gz.
But can Slicer change the resolution without having to resort to that tool? And if it does, does it do the interpolation, or does it simply downsample?
Thanks,


Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 16:00:27 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Mmmmm

that does not have an easy answer I guess. That export feature is not yet implemented. What tools do you want to interact with?

D

--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:59 PM, shoosh moosh wrote:

Great, thanks!
Now how do I convert from a DTI that is in (*.nhdr  & *.raw.gz) format to a DTI that is in *.nii.gz format?
Thanks



Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 15:34:06 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Hi!

On the Diffusion menu -> Utilities there is one called Diffusion Tensor Estimation.

You can find all the details regarding the process in:

Happy to help
Demian




--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:30 PM, shoosh moosh wrote:

How do I convert from diffusion weighted image (*.nrrd format) to Diffusion tensor image in slicer?
Thanks

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject



_______________________________________________ slicer-users mailing list [hidden email] http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________ slicer-users mailing list [hidden email] http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: Converting from DWI to DTI

Francois Budin-2
Resample DTI Volume does not do the interpolation in the log-euclidean space due to uncertainties about possible patents.

Francois

2010/9/21 shoosh moosh <[hidden email]>
Does the Resample DTI Volume module do the interpolation Log-Euclidean?
Thanks


Date: Wed, 15 Sep 2010 15:49:36 -0400
From: [hidden email]
To: [hidden email]
Subject: Re: [slicer-users] Converting from DWI to DTI

There is a module called "Resample DTI Volume" under Diffusion->Utilities with various interpolation types available.

On your original question of .nii.gz format: as far as I know, Slicer does not support writing tensor volumes as Nifti (nii). From a quick look, it seems like the underlying library (ITKNiftiImageIO) supports writing the necessary datatype NIFTI_INTENT_SYMMATRIX --so you could probably do  in tcl/python. Another route would be to reshape the raw file and build a header using fslcreatehd

More generally, if you are doing analysis in another program it will be easier to just converdirectly t nii from the original DICOM images if you have them (uing ie: mri_convert from FreeSurfer, dcm2nii, mricro/n, etc..).

-Isaiah

On 09/15/2010 03:13 PM, shoosh moosh wrote:

Actually I needed it in that format in order to change its resolution from (1x1x3) to (1x1x1). I found this TVResample module in DTI Toolkit that requires the DTI volume to be in *.nii.gz.
But can Slicer change the resolution without having to resort to that tool? And if it does, does it do the interpolation, or does it simply downsample?
Thanks,


Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 16:00:27 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Mmmmm

that does not have an easy answer I guess. That export feature is not yet implemented. What tools do you want to interact with?

D

--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:59 PM, shoosh moosh wrote:

Great, thanks!
Now how do I convert from a DTI that is in (*.nhdr  & *.raw.gz) format to a DTI that is in *.nii.gz format?
Thanks



Subject: Re: [slicer-users] Converting from DWI to DTI
From: [hidden email]
Date: Wed, 15 Sep 2010 15:34:06 -0300
CC: [hidden email]; [hidden email]
To: [hidden email]

Hi!

On the Diffusion menu -> Utilities there is one called Diffusion Tensor Estimation.

You can find all the details regarding the process in:

Happy to help
Demian




--
Demian Wassermann, PhD
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Sep 15, 2010, at 3:30 PM, shoosh moosh wrote:

How do I convert from diffusion weighted image (*.nrrd format) to Diffusion tensor image in slicer?
Thanks

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject



_______________________________________________ slicer-users mailing list [hidden email] http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________ slicer-users mailing list [hidden email] http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users To unsubscribe: send email to [hidden email] with unsubscribe as the subject

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject