Hi Peter,
Thank you for delivering the good news. I tried to compile new release of
MITK from the source code in order to get MitkDiffusion and MiniApps. And I
got some errors ³Ignoring unknown target ³org_mitk_diffusionImaging² for
installation². I guess I have to wait the formal release of MitkDiffusion.
Wayne
On 14-04-16 6:13 AM, "Peter Neher" <[email protected]> wrote:
> Hi Wayne,
>
> I think the new release of MITK will support the trackvis file format, at
> least if you perform the tracking using the MiniApp command line tool.
> But to include the geometry of the image in the output file will only work
> for the miniApp, not the GUI application. In the miniApp it is possible to
> directly associate the image with the tractogram, which is in general not
> possible in the GUI. The new release of MitkDiffusion will be available soon
> and hopefully also the MiniApps.
>
> Cheers,
> Peter
>
>
> On 04/11/2014 10:19 PM, Wayne Su wrote:
>
>
>> Re: Save Fiber bundle TrackVis uses LPS coordinate system. But the fiber
>> bundle saved by MITK uses RAS coordinate system. I managed to edit the
>> dimension of track file, and translate x and y values in the track file.
>> Finally I got aligned track and DWI in TrackVis program.
>>
>> If I¹m correct, I suggest to save TrackVis track file in LAS instead RAS
>> coordinate system. And use the full dimension of upsampled DWI in 1x1x1
>> resolution, or maybe native DWI space. All this needs to modify MITK source
>> code.
>>
>> Wayne
>>
>>
>> On 14-04-11 8:50 AM, "Wayne Su" <[email protected]> wrote:
>>
>>
>>> Hi Christian,
>>>
>>> Thank you for the reply. In the MITK-DT, the fiber bundle aligns well with
>>> T1 and DWI. What I¹m trying is to load them into TrackVis. Because the
>>> dimension of the fiber bundle is no longer same as the one from DWI, they
>>> don¹t align in TrackVis. I¹m wondering whether there is any option to use
>>> the dimension of DWI (maybe the upsampled DWI with 1x1x1 resolution) to save
>>> fiber bundle. I know there are two ways. One solution is to crop DWI to
>>> match fiber bundle. Another way is to change the dimension of fiber bundle
>>> (I¹m not familiar with this part). I appreciate any input on this case.
>>>
>>> Thanks,
>>> Wayne
>>>
>>>
>>> On 14-04-11 12:56 AM, "Weber, Christian(1)" <[email protected]>
>>> wrote:
>>>
>>>
>>>> Hi Wyane,
>>>>
>>>> the fiber bundles are allways in the space of DWI since they are derived
>>>> from it.
>>>> Since DWI and T1/T2 often do not match you need to register them,
>>>> currently the easiest way doing this with GUI is
>>>> (AFAIK ):
>>>>
>>>> Extract B0 image from the DWI and then register the T1 to this B0 image,
>>>> using e.g. the Point-Based registration.
>>>>
>>>> Best,
>>>> Christian
>>>>
>>>>
>>>> From: Wayne Su [mailto:[email protected]]
>>>> Sent: Donnerstag, 10. April 2014 20:10
>>>> To: [email protected]
>>>> Subject: [mitk-users] Save Fiber bundle
>>>>
>>>> Hello experts,
>>>> Is there a way to save diffusion fiber bundle onto T1 structural space or
>>>> DWI space, i.e. the dimension of the fiber bundle is the same as the one
>>>> from T1 or DWI? Currently, it saves as reduced dimension with 1mmx1mmx1mm
>>>> spacing. I tried to load the track file into TrackVis along with T1 image.
>>>> But the locations of them don¹t match.
>>>>
>>>> Thanks,
>>>> Wayne
>>>>
>>>>
>>>
>>
>
>
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