[slicer-users] Help regarding DICOM files

Andras Lasso lasso at cs.queensu.ca
Tue Jul 13 08:27:25 EDT 2010


I assume that you would process the exported text file by a software, so why don't you extend the LabelStatistics module with the functionality that you need? Just modify vtkLabelStatisticsLogic::Apply() to compute the data you need (or implement saving of the voxel values into a text file there). If you implemented something that might be useful for others, then you could even commit it to the Slicer repository.

Andras

-----Original Message-----
From: slicer-users-bounces at bwh.harvard.edu [mailto:slicer-users-bounces at bwh.harvard.edu] On Behalf Of Saurabh Gupta 402549
Sent: July-13-10 3:49 AM
To: Isaiah Norton; slicer-users at bwh.harvard.edu
Subject: Re: [slicer-users] Help regarding DICOM files

Yes it would. But it just gives the min, max, volume, std dev. Is there a way by which you can get all the HU values in a text file for all the pixels that fall under a marked label ?

Saurabh

-----Original Message-----
From: slicer-users-bounces at bwh.harvard.edu [mailto:slicer-users-bounces at bwh.harvard.edu] On Behalf Of Isaiah Norton
Sent: Monday, July 12, 2010 8:11 PM
To: slicer-users at bwh.harvard.edu
Subject: Re: [slicer-users] Help regarding DICOM files

The "label statistics" module will save information to a text file.

-Isaiah

On 07/12/2010 10:20 AM, Saurabh Gupta 402549 wrote:
> Ok
>
> What if I wanted to take HU values and corresponding pixels in a text file ?
>
> Regards
> Saurabh
>
> -----Original Message-----
> From: Andriy Fedorov [mailto:fedorov at bwh.harvard.edu]
> Sent: Monday, July 12, 2010 6:27 PM
> To: Saurabh Gupta 402549
> Cc: slicer-users at bwh.harvard.edu
> Subject: Re: Help regarding DICOM files
>
> Hi Saurabh,
>
> I will try to answer, but for the future please direct these kind of
> questions to the Slicer user list: slicer-users at bwh.harvard.edu
>
> On Mon, Jul 12, 2010 at 08:12, Saurabh Gupta 402549
> <Saurabh_402549 at infosys.com>  wrote:
>    
>> Hi Andriy Fedorov
>>
>>
>>
>> You might remember that I sent a mail regarding the error in loading the
>> DICOM files in Slicer. I converted the DICOM files into NRRD and it loads
>> fine. However, since I am new to this, I had certain queries. I would be
>> really thankful if you can answer them.
>>
>>
>>
>> 1.       Is there a way by which we can read the HU values from the DICOM
>> images (pixel by pixel)?
>>
>>      
> The NRRD file you load should contain the same HU values as in the
> original DICOM file.
>
> If you want to simply "read" these values, you can do so by moving the
> mouse pointer over the specific pixel, and reading the value Slicer
> reports to you in the slice viewer.
>
> If you want to compute statistics over the HU values in a region, you
> can do this by creating a label image in the editor module
>
> http://wiki.slicer.org/slicerWiki/index.php/Modules:Editor-Documentation-3.6
>
> and use Label Statistics module
>
> http://wiki.slicer.org/slicerWiki/index.php/Modules:LabelStatistics-Documentation-3.6
>
> to get the mean and variance for the HU values within the label you created.
>
>
>    
>> 2.       Since there are other regions as well apart from the required
>> portion, I created a label in Slicer and marked the areas. I then converted
>> it into a model using Model Maker. However it seems that this creates a
>> solid model and the original intensity/ grey value information is lost. Is
>> it possible to know the HU value from this vtk file ?
>>
>>
>>      
> There is no need to create a model to calculate greylevel statistics.
> Please follow the approach I described above. If I misunderstood your
> question, please reply to the list.
>
>    
>> I know my doubts might sound naïve but I am unable to get a clear
>> understanding of this thing. My objective is to get the HU values from the
>> areas of interest but I am unsure how to do that.
>>
>>      
> No problem.
>
> Please let us know if this does not answer your question.
>
> AF
>
>
>    
>>
>> Regards
>>
>> Saurabh
>>      
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