[slicer-users] question about file formats

Demian Wassermann demian at bwh.harvard.edu
Thu Jun 30 07:27:54 EDT 2011


Hello Kathleen and Sonia,

Katheleen, 

Usually the output of a DTI scan is a set of Diffusion Weighted Images (DWI) and not a proper Diffusion Tensor Image (DTI) which is obtained after processing all the DWI files.

If by export to NIFTI you mean exporting the DWI images, which is the most probable scenario, you will not be able to import it to Slicer. You can check this by observing if the output is a set of 55 files (or file pairs) or a single NIFTI with 55 time points.

There is no standard format for DWI in NIFTI, that's why it is not implemented in Slicer and we are going with the standardized DICOM format. Several tools allow you to convert the DWI to DTIs, but each one of these tools has a different way of interpreting the DWIs and they will need you to obtain the gradient directions somehow, usually from the DICOM images.

Even if it looks cumbersome, I'd recommend to download these images to DICOM to a DVD or something and from DICOM, calculate the DWI images with Slicer and subsequently DTIs. The conversion in slicer is  very good at preserving all the needed data that comes out from the scanner (in the DICOM format) and use it to obtain a good DTI image.

Hope that helps
Demian

--
Demian Wassermann, PhD
demian at bwh.harvard.edu
LMI / PNL / SPL Labs
Harvard Medical School
Brigham and Women's Hospital
1249 Boylston, Boston, MA, USA

On Jun 29, 2011, at 7:09 PM, Sonia Pujol wrote:

> Kathleen,
> 
> We have added two new modules in Slicer for importing and exporting tensor data in Nifti. The modules are called 'DTIimport' and 'DTIexport', and they should be part of the Slicer3-3.6.4-beta-2011-06-30 nightly build.
> 
> I hope this helps,
> 
> Best Regards,
> 
> Sonia
> 
> 
> On 6/29/11 5:42 PM, Kathleen Friel wrote:
>> 
>> Hi Slicers,
>> 
>> I have a question about file formats.  I have done some DTI scans on a Phillips 3T, 55 directions.  I am having some problems with my files.  On the scanner, I am having trouble exporting the files as DICOMs.  (There are 4275 total files per subjects.)  We're figuring that out!  As a backup plan, I was wondering...
>> 
>> - Is it possible for Slicer to read and analyze par/rec files?
>> - Is it possible for Slicer to read and analyze nifti or analyze files? (I am able to export my files as niftis.)
>> - Does anyone know of a par/rec to dicom converter?
>> 
>> Thanks very much for any help you can provide!
>> Kathleen
>> 
>> 
>> Kathleen Friel, Ph.D.
>> Assistant Professor of Clinical Psychiatry
>> Division of Brain Stimulation and Therapeutic Modulation
>> Department of Psychiatry 
>> Columbia University Medical Center
>> 1051 Riverside Drive, Unit 21
>> New York, NY 10032
>> (212) 543-6907
>> kf2105 at columbia.edu
>> http://www.brainstimulation.columbia.edu/staff/bio_friel.html
>> 
>> 
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> 
> 
> -- 
> Sonia Pujol, Ph.D.
> Surgical Planning Laboratory, Harvard Medical School
> Brigham and Women's Hospital, Boston, MA
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