Slicer volume loading issues

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Slicer volume loading issues

Kyzyl Herzog
Hello all,

I'm very new to Slicer (3.4.1.0, win32). I've been attempting to load MRI volumes of various formats, with no luck. I assume I'm just doing something wrong, but I haven't been able to solve my problem via the documentation. I want to load my data set (I have my data in many formats) in this order of preference:

1. Straight binary PAR/REC files from a Philips scanner; uint16, little endian byte order, no header (this seems unrealistic ;-)
2. Directory organized image sequences (i. tiff, ii. png, iii. jpg, iv. whatever else)
3. DICOM volumes (lower preference because I only have my earlier patient data in this format)

So far I have only been able to load (File->Add Volume) the tiff sequences. However, the image is displaying as a binary mask (just black and gray), although the histogram and data type (unsigned short) say otherwise. When I attempt to load the DICOM volumes, it parses the directories but doesn't produce a tree, and won't load ('Apply').

I'm sure I'm just missing something simple, but any help would be appreciated.

FYI: I'm attempting to load sets of 8 DTI images (256x256x12) and 75 DCE images (256x256x12).

Thanks,
Kyzyl
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Re: Slicer volume loading issues

pieper
Administrator
Hi Kyzyl -

Slicer doesn't have any PAR/REC support, but you should be able to
convert to nifti (check google or nitrc.org).  Or you could go directly
to .nrrd format (slicer's preferred dti format) using the CATNAP tool:

http://godzilla.kennedykrieger.org/~jfarrell/software_web.htm

For the tiff/png/jpg files, they should load as something like
image001.png, image002.png, etc.  But if they are RGB they won't work
with several of the slicer tools that expect grayscale (one component) data.

Older DICOM data sometimes won't load with the reader software slicer
uses (GDCM from ITK).  You may be able to use another tool to load the
dicoms and export as a volume format (nrrd, nifti, etc).

Best,
Steve


On J/29/10 2:30 PM, Kyzyl Herzog wrote:

> Hello all,
>
> I'm very new to Slicer (3.4.1.0, win32). I've been attempting to load
> MRI volumes of various formats, with no luck. I assume I'm just doing
> something wrong, but I haven't been able to solve my problem via the
> documentation. I want to load my data set (I have my data in many
> formats) in this order of preference:
>
> 1. Straight binary PAR/REC files from a Philips scanner; uint16, little
> endian byte order, no header (this seems unrealistic ;-)
> 2. Directory organized image sequences (i. tiff, ii. png, iii. jpg, iv.
> whatever else)
> 3. DICOM volumes (lower preference because I only have my earlier
> patient data in this format)
>
> So far I have only been able to load (File->Add Volume) the tiff
> sequences. However, the image is displaying as a binary mask (just black
> and gray), although the histogram and data type (unsigned short) say
> otherwise. When I attempt to load the DICOM volumes, it parses the
> directories but doesn't produce a tree, and won't load ('Apply').
>
> I'm sure I'm just missing something simple, but any help would be
> appreciated.
>
> FYI: I'm attempting to load sets of 8 DTI images (256x256x12) and 75 DCE
> images (256x256x12).
>
> Thanks,
> Kyzyl
>
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject