[ITK] [ITK-users] Read 4D CT cardiac dicom series and save it as a single 4D nifti file

[marco giordano]

Dear Andras, all,
I did try with 3D Slicer but the 4D sequence is not loaded correctly
(slices are not loaded in the right order). One issue that I see is that
each Dicom series is actually a semi-volume (e.g. the upper or lower part
of a volume) thus it requires some merging of the data before writing. I am
writing some code even though I thought there would be more examples of
similar import routine developed in the past. I will keep you posted if i
make any progress
regards



2016-06-11 6:25 GMT+02:00 Andras Lasso <lasso at queensu.ca>:

> 3D Slicer can load some 4D CTs a 3D+t sequence and you cab save it as a 4D
> nrrd. You may give it a try. If it doesn't work for your sequence then
> report the problem on the slicer-users mailing list. If you can provide a
> sample data set then slicer developers most likely will be able to make it
> work.
>
>
>
> Andras
>
>
>
> *From: *marco giordano <marco.giord at gmail.com>
> *Sent: *June 10, 2016 17:32
> *To: *Scapegoat Sarthak <scapegoat.sarthak at gmail.com>
> *Cc: *insight-users at itk.org
> *Subject: *Re: [ITK] [ITK-users] Read 4D CT cardiac dicom series and save
> it as a single 4D nifti file
>
>
> Hi there,
>
> Thanks for the suggestions. VV is not really an option since I have to
> analyze many cases. I even tried to use VV but it gives me the wrong order
> of the slices.
>
> I am trying the  "itk::ImageSeriesReader" (right?) but it is complaining
> that "Position is not unique".  I think it refers to the fact that the
> slices in my "series" have the "same location". Not sure this is meant to
> transform 2D into 4D if it expects different locations, maybe it is for 2D
> into 3D. Any idea?
>
> Regards
>
> 2016-06-09 17:21 GMT+02:00 Scapegoat Sarthak <scapegoat.sarthak at gmail.com>
> :
>
>> You can do it pretty easily:
>>
>> Read DICOM using SeriesFileReader and then connect output to a FileWriter
>> with the file name of your choice (in this case, it would be
>> "output.nii.gz").
>>
>>
>> On 9 June 2016 at 11:06, Mohammad Varasteh <varasteh at to.infn.it> wrote:
>>
>>> Dear Marco,
>>>
>>> Actually I do not know how to do it in the ITK but for such cases (if it
>>> is
>>> few cases) I normally use "VV: the 4D slicer". You can find it in the
>>> following link:
>>>
>>> http://www.creatis.insa-lyon.fr/rio/vv
>>>
>>> I hope this will be of some use.
>>>
>>> Varasteh
>>>
>>>
>>>
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>
>
> --
> Marco Giordano
> SKYPE:marcogiord81
>



-- 
Marco Giordano
SKYPE:marcogiord81
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