[Camino-users] PARAVIEW visualization issue

Mon Oct 14 06:04:48 PDT 2013

Hi again Michael,
still I am not totally happy with the palette issue, but at least now I
know that it was not a problem of my data in a way.
Thanks again for replying me!
Best,
Alessandro

2013/10/13 Michael <mdayan.research at gmail.com>

> 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>
>>
>>
>

-- 
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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