[Mristudio-users] Beginning DTIStudio

[Raj Jaswal]

---------- Forwarded message ----------
From: Raj Jaswal <raj.jaswal at gmail.com>
Date: Mon, Oct 20, 2008 at 2:34 PM
Subject: Beginning DTIStudio
To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <
mristudio-users at mristudio.org>, "support at mristudio.org" <
support at mristudio.org>


Hi all,

  I am relatively new to the realm of DTI and imaging in general. Any help
from anyone would be greatly appreciated!
  I'm having some difficulty in taking my raw images (from a 3T Siemens) and
doing the DTI Mapping and Fiber Tracking through DTIStudio.

  The first thing I do is use DicomWorks software to convert the raw data
from the Siemens machine into a structured DICOM format.
  I have two sets of DTI data from the machine:
        * Set 1 is 32 slices with a 5mm thickness using 12 gradient
directions (416 total files)
        * Set 2 is 50 slices with a 3mm thickness using 12 gradient
directions (650 total files)

  I am trying to analyze Set 1 first. The process I go through is the
following (Please correct me if I am wrong anywhere!):

  1. File --> DTI Mapping (I select "Siemens, GE, or Philips DICOM" and
click Continue)
  2. I use the gradient table provided by mristudio.org and select the first
12 gradients under Siemens DICOM (Lines 0-11).
  3. b-Value is 700. And I add the folder of Set 1 to the "DICOM Image-File
Folders" section and click OK.
  4. All 416 files are processed and just to check, I get 13 files in the
drop down box in the Image tab (12 gradients + 1 b0)
  5. I click on the "DtiMap" tab and click on the "Original - ADC - Mean -
STD" button to view the images. (12 images due to gradients)
  6. Next, I click on the "Tensor, Color Map etc." button in order to
perform the tensor calculation. I leave the noise level at 10 and leave
"Consider B-Value" checked. The other options I do not change. Click OK. At
the Automatic Outlier Rejection window I click "No". (32 slices are being
processed).
  7. I go back to the "Image" tab and save the following files:
      7a. Anisotropy-FA --> test.FA
      7b. color map 0 --> test.color
      7c. eigenvector 0 --> test.vec
      7d. tensor images (all 6) --> test.d
      7e. dwi file --> test.dwi
      7f.  b0 file --> test.b0
      7g. eigenvalue 0 file --> test.ev0

  8. File --> Fiber Tracking. I load the test.FA and test.vec files with
image dimensions of 128x128 and Voxel size of 64x64 with a 5mm thickness.
The rest options are default for now.
  9. I click on the "Color Map" button select both the .fa and .vec files
and click OK.
  10. I then click on the "Fiber" tab and check off ""show items in 2D
image", "roi drawing enable", and "user defined".
  11. I proceed to draw an arbitrary ROI in the image in the top-right
quadrant.
  12. The area selected has 16 fibers (according to statistics button). I
click on the save icon next to the "FACT" button.
  13. I click on the save icon under the "ROI - Operation" section as well.
I save it as the Graphic Compatible (Default) option.

  14. From here, I open ROI Editor and load the "test.FA" file and set the
image dimension to 128x128 (32 slices) and the voxel size to 64x64 with a
slice thickness of 5mm. The image data format is selected as type Float.

  I can attach screenshots of what I get after steps 8, 9, and 14. If
possible, can anyone let me know if I'm on the right track or if there is
anything wrong with what I am doing? Also, is there an instruction set or
tutorial for using ROIEditor and LandMarker?
Thank you very much for your time.

  - RJ


-- 
- RJ



-- 
- RJ
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