DTI to NRRD

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

DTI to NRRD

Christian Schmidt
Hello,

i got DTI data from the brain for my research (406 slices). I tried the
Dicom to Nrrd Converter like in the DTI tutorial but it terminated with
an error.

ERROR: In
..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line
1660
vtkCommandLineModuleLogic (10D305C8): Dicom to Nrrd Converter terminated
with an unknown exception.


When i try to load them as a volume, slicer tells me that the images are
not equally spaced.

Regards,
Christian

_______________________________________________
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: DTI to NRRD

Xiaodong Tao-2
Which version of Slicer are you using? And what are the output of DicomToNrrdConverter?

Thanks.
Xiaodong

-----Original Message-----
From: [hidden email] on behalf of Christian Schmidt
Sent: Wed 6/22/2011 11:27 AM
To: [hidden email]
Subject: [slicer-users] DTI to NRRD
 
Hello,

i got DTI data from the brain for my research (406 slices). I tried the
Dicom to Nrrd Converter like in the DTI tutorial but it terminated with
an error.

ERROR: In
..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line
1660
vtkCommandLineModuleLogic (10D305C8): Dicom to Nrrd Converter terminated
with an unknown exception.


When i try to load them as a volume, slicer tells me that the images are
not equally spaced.

Regards,
Christian

_______________________________________________
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: DTI to NRRD

Christian Schmidt
In reply to this post by Christian Schmidt
Hello,

i managed to convert the Dicom files to nifti files (b0 volume, 6
direction volumes, bval file and bvec file) and i can open the b0 and
the direction volumes with slicer. Is there any way to convert them to a
nrrd file? My desired output is a DTI nrrd file with the 3x3 tensors and
the space dimensions. Could it be (that easy) that the direction volumes
are the entries of the tensor (symmetric aligned)?

With kind regards,
Christian

Am 22.06.2011 17:27, schrieb Christian Schmidt:

> Hello,
>
> i got DTI data from the brain for my research (476 slices). I tried the
> Dicom to Nrrd Converter like in the DTI tutorial but it terminated with
> an error.
>
> ERROR: In
> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line
> 1660
> vtkCommandLineModuleLogic (10D305C8): Dicom to Nrrd Converter terminated
> with an unknown exception.
>
>
> When i try to load them as a volume, slicer tells me that the images are
> not equally spaced.
>
> Regards,
> Christian
>

_______________________________________________
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: DTI to NRRD

inorton
Hi Christian,

1. if it is possible to provide more debugging information please Slicer version and  DicomToNrrd output (in Window->Error Log). This would be the best option. Also, if it is possible to share a dataset that would be helpful for debugging.

2. if you want to try the conversion from fsl nifti dwi, see below... mileage may vary.

> Could it be (that easy) that the direction volumes are the entries of the tensor (symmetric aligned)?

The DWI direction volumes should represent different acquisitions with varied gradient directions. Tensors must be fitted to create the DTI volume, which can be done in Slicer after you create a DWI volume.

There is no simple method to convert the fsl nifti DWI convention (nii+bvec+bval) into Slicer nrrd DWI format, but an outline of the process is available here:

http://slicer-users.65878.n3.nabble.com/GTract-V4-questions-td2805165.html

HTH,
-Isaiah

On Thu, Jun 23, 2011 at 5:04 AM, Christian Schmidt <[hidden email]> wrote:
Hello,

i managed to convert the Dicom files to nifti files (b0 volume, 6
direction volumes, bval file and bvec file) and i can open the b0 and
the direction volumes with slicer. Is there any way to convert them to a
nrrd file? My desired output is a DTI nrrd file with the 3x3 tensors and
the space dimensions. Could it be (that easy) that the direction volumes
are the entries of the tensor (symmetric aligned)?

With kind regards,
Christian

Am 22.06.2011 17:27, schrieb Christian Schmidt:
> Hello,
>
> i got DTI data from the brain for my research (476 slices). I tried the
> Dicom to Nrrd Converter like in the DTI tutorial but it terminated with
> an error.
>
> ERROR: In
> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line
> 1660
> vtkCommandLineModuleLogic (10D305C8): Dicom to Nrrd Converter terminated
> with an unknown exception.
>
>
> When i try to load them as a volume, slicer tells me that the images are
> not equally spaced.
>
> Regards,
> Christian
>

_______________________________________________
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