[Camino-users] PARAVIEW visualization issue

[Michael]

I also had this strange issue when translation was only needed along the
x-axis and i'd still need to investigate further to explain what's
happening. However if the images fit fine after you applied an
x-translation as according to the header this should be a correct
alignment.

I don't have any issue applying a slice filter after a transform filter so
i cannot really help you with this.

Applying a different colour scale to different volumes is not an intuitive
process in Paraview: you need to use the calculator filter for each of the
volume for which you'd like a specific colour scale. Select Calculator
filter, then "Scalars"menu and choose the field for which you want to map
the voxel values. Then change the array name from "Result" to any unique
name, say "my_values". After clicking "Apply" you'll see that the field
"color" is now associated to "my_values" to which you can associate any
colour scale without changing your other volumes.


On Sun, Oct 13, 2013 at 6:08 AM, Alessandro Calamuneri <
alecalamuneri at gmail.com> wrote:

> Hi Michael,
> I have obtained really weird results: applying such tranformation (the one
> you described and, that I was supposing being the proper one as well), FA
> and tracts do not align correctly. Whereas if I just apply a translation
> along x axis of 90 (without considering the negative sign in the scaling
> factor) things go well.
> I also tried to apply the same transformation to both image and vtk
> object, getting an error for FA map (it came out with an impossibility to
> find a slice rapresentation for a transformed object, which may in a way
> make sense, as I don't know how paraview apply its transformation).
> Then at the moment I am really skeptical for my visualization results, as
> they seem to follow random rules.
> Maybe there is something wrong in my FA map, that is reflected into the
> vtk object, but I do not see the problem, as everything otherwise is fine.
> I have also overlapped my seed image to better localize my tract origin: I
> had to transform my seed as a volume (which was ok as it was only a voxel
> placed in the CST), and everything was fine just after appliyng x
> translation
> (I would like also to ask you whether there is a way to edit the colour
> map of a single nifti file keeping the standard gray one for others; I am
> asking that because when I tried to do it for my nifti seed volume to
> better highlight it, it resulted in a modifications of all the palettes of
> my brain volumes.)
> Hoping to not have bored you with my long message, and hoping you could
> explain me better the reasons of such random results,
> Best Regards
> Alessandro
>
>
> 2013/10/12 Michael <mdayan.research at gmail.com>
>
>> Hi Alessandro, you only have to fill the translation parameters with
>> values 90, -126 and -72 for x, y and z parameters respectively. Note that
>> you may have to multiply these values by 2 (as indicated by the scaling
>> factor in your matrix) and use -90 instead of 90 for your x translation
>> parameter.
>>  On Oct 11, 2013 5:36 PM, "Alessandro Calamuneri" <
>> alecalamuneri at gmail.com> wrote:
>>
>>> Hi Michael,
>>> thanks a lot for replaying soon!
>>> I am a bit into troubles for applying the trasformation, because in the
>>> header information I get a 4x4 matrix with the spatial information,
>>> something like
>>> -2 0 0 90
>>> 0 2 0 -126
>>> 0 0 2 -72
>>>
>>> When I get into the transform function within paraview I am asked 3
>>> values for translation, 3 for rotation and 3 for scaling.
>>> How should I correctly fill out those parameters? To me it is not that
>>> clear
>>> Best,
>>> Alessandro
>>>
>>>
>>> 2013/10/10 Michael <mdayan.research at gmail.com>
>>>
>>>> Hi Alessandro,
>>>>
>>>> I have exactly the same issue but couldn't solve it using
>>>> vtkstreamlines. As a temporary fix (which worked for me) you could apply a
>>>> transform to your tracts in Paraview (Filter --> Alphabetical -->
>>>> Transform) to align them with your FA image, the transform parameters being
>>>> in your image header. You can read the header of your Analyze image with
>>>> "analyzeheader -readheader <image>" or your NIFTI image with "niftiheader
>>>> -readheader <image>"
>>>>
>>>>
>>>> On Thu, Oct 10, 2013 at 12:27 PM, Alessandro Calamuneri <
>>>> alecalamuneri at gmail.com> wrote:
>>>>
>>>>> Hi all,
>>>>> I'm new to Camino toolbox. I run deterministic tractography on a seed
>>>>> region, and would like to visualize results using paraview overlaying my FA
>>>>> map and the track. I use vtkstreamlines command to convert my track file,
>>>>> and open both FA image and the tracks. I represent Fa image as slice, and
>>>>> the tracts as wireframe; even if directional informations seem to be ok for
>>>>> correctly color coding tracts, two objects do not overlay at all. It is
>>>>> probably due to the loss of header informations after running track
>>>>> command. How do you link again such infos to the streamline in vtk format?
>>>>> I'm sure there is a way, as you have displayed in the tutorial.
>>>>> Thanks
>>>>> Alessandro
>>>>>
>>>>> --
>>>>> Alessandro Calamuneri
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Camino-users mailing list
>>>>> Camino-users at www.nitrc.org
>>>>> http://www.nitrc.org/mailman/listinfo/camino-users
>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> Alessandro Calamuneri
>>> M. Sc., PhD-student in Ricerca Clinica e Traslazionale in Neuroscienze
>>> ed Oncologia
>>> Dipartimento di Neuroscienze, Scienze Psichiatriche e Anestesiologiche
>>> Policlinico Universitario "G.Martino"
>>> Università degli Studi di Messina
>>> tel: 0039 346 23 77 151
>>> mail: alecalamuneri at gmail.com
>>>         alessandro.calamuneri at unime.it
>>>         alecalamuneri at hotmail.it <alecalamuneri at tiscali.it>
>>>
>>>
>
>
> --
> Alessandro Calamuneri
> M. Sc., PhD-student in Ricerca Clinica e Traslazionale in Neuroscienze ed
> Oncologia
> Dipartimento di Neuroscienze, Scienze Psichiatriche e Anestesiologiche
> Policlinico Universitario "G.Martino"
> Università degli Studi di Messina
> tel: 0039 346 23 77 151
> mail: alecalamuneri at gmail.com
>         alessandro.calamuneri at unime.it
>         alecalamuneri at hotmail.it <alecalamuneri at tiscali.it>
>
>
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