[Insight-users] [slicer-users] need help

[Sylvain Jaume]

Hi Ahmed,

Slicer uses the spacing of image to map the slices (coronal, axial and
sagittal) to the screen. In the upper right corner of the coronal view
you can see the spacing between coronal slices. You will see the
spacing between axial slices and between sagittal slices when you
hover your mouse over the axial view and over the sagittal view
respectively. Slicer did not resample your volume to 256x256x256 but
map the slice with its correct spacing to the screen (e.g.
0.5mmx0.938mm in axial view, 0.938mmx0.5mm in sagittal view and
0.5mmx0.5mm in coronal view).

Your screenshots show that Matlab did not use the spacing and
therefore the display is not correct. Additionally when you are
passing your software to a clinician or another student, you are
forcing them to have a Matlab license. This is often too expensive and
thus limits the impact of your software. I recommend you use Slicer
and not Matlab to prototype your algorithms because:

  - it will save you the burden of later porting your code to a
software platform that clinicians can use, and
  - it will save the citizens to pay for the porting of your code and
to wait even longer to benefit for the research they have already
funded when you were coding in Matlab.

  In a field where duration of a project can be counted in number of
lives lost, coding in Matlab is irresponsible.

Best regards,
Sylvain


Sylvain Jaume, Ph.D.
MIT Computer Science and Artificial Intelligence Laboratory
32 Vassar Street 32-D430, Cambridge MA 02139, USA


On Wed, Feb 3, 2010 at 4:53 AM, Ahmed Shaibal <shaibal125 at yahoo.com> wrote:
> Hi Sylvain
>
> Thank you for your mail. Actually my question was what are the size of
> coronal and axial images. The sagittal image has of course size
> 256-by-256-by-124 (this is what is shown in 'info'). I think axial and
> coronal images should have size 256-by-124-by-256. what do you think? But
> from the 2D viewer it seems like they are 256-by-256-by-256. Do you have any
> idea how the images are resized (dont confuse it with interpolation check
> box for rendering)?
>
> I have attached couple of images, one of them views the volumes in slicer
> and the other one is the figure I got with matlab. Notice how the coronal
> and axial slice is squeezed left to right. It is because the number of
> columns for them is smaller than sagittal slice.
>
> regards
>
> Ahmed Mostayed
> PhD Student
> Intelligent Systems for Medicine Lab (ISML)
> Dept of Mechanical Engineering
> The University of Western Australia
> 35 Stirling highway, Crawley-Perth, WA-6009
> Tel. +61430911286 Email. mostayed at mech.uwa.edu.au
>
> ________________________________
> From: Sylvain Jaume <sylvain at csail.mit.edu>
> To: Ahmed Shaibal <shaibal125 at yahoo.com>
> Cc: slicer-users at bwh.harvard.edu
> Sent: Wednesday, February 3, 2010 5:52:51
> Subject: Re: [slicer-users] need help
>
> Hello Ahmed,
>
> Could you check the volume dimensions under Modules > Volumes > Info ?
> What index do you see in the upper left corner for each view?
>
> In case you are confused about the inter-voxel interpolation for
> rendering, you can uncheck the Interpolate checkbox under Modules >
> Volumes > Display.
>
> Regards,
> Sylvain
>
> On Tue, Feb 2, 2010 at 4:01 PM, Ahmed Shaibal <shaibal125 at yahoo.com> wrote:
>> Hi
>>
>> I am a new user. I just finished a tutorial on 3D data loading and
>> visualization. In this tutorial a DICOM format volume is loaded. The
>> volume
>> size is 256-by-256-by-124. That means it has 124 sagittal slices each
>> having
>> resolution 256-by-256. and the coronal and axial slices should be
>> 256-by-124.  But from the 2D view it looks like that axial and coronal
>> slices also have resolution 256-by-256. Seems like slicer does some kind
>> of
>> interpolation to resize those two slices. can anyone tell me what is that
>> exactly or refer to any documentation?
>>
>> waiting for feedback.
>> regards.
>>
>>
>>
>> Ahmed Mostayed
>> PhD Student
>> Intelligent Systems for Medicine Lab (ISML)
>> Dept of Mechanical Engineering
>> The University of Western Australia
>> 35 Stirling highway, Crawley-Perth, WA-6009
>> Tel. +61430911286 Email. mostayed at mech.uwa.edu.au
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