<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Raj Jaswal</b> <span dir="ltr"><<a href="mailto:raj.jaswal@gmail.com">raj.jaswal@gmail.com</a>></span><br>
Date: Mon, Oct 20, 2008 at 2:34 PM<br>Subject: Beginning DTIStudio<br>To: "DTI Studio, ROI Editor, Landmarker Questions/Support" <<a href="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</a>>, "<a href="mailto:support@mristudio.org">support@mristudio.org</a>" <<a href="mailto:support@mristudio.org">support@mristudio.org</a>><br>
<br><br><div dir="ltr">Hi all,<br><br> I am relatively new to the realm of DTI and imaging in general. Any help from anyone would be greatly appreciated!<br> I'm having some difficulty in taking my raw images (from a 3T Siemens) and doing the DTI Mapping and Fiber Tracking through DTIStudio.<br>
<br> The first thing I do is use DicomWorks software to convert the raw data from the Siemens machine into a structured DICOM format.<br> I have two sets of DTI data from the machine:<br> * Set 1 is 32 slices with a 5mm thickness using 12 gradient directions (416 total files)<br>
* Set 2 is 50 slices with a 3mm thickness using 12 gradient directions (650 total files)<br><br> I am trying to analyze Set 1 first. The process I go through is the following (Please correct me if I am wrong anywhere!):<br>
<br> 1. File --> DTI Mapping (I select "Siemens, GE, or Philips DICOM" and click Continue)<br> 2. I use the gradient table provided by <a href="http://mristudio.org" target="_blank">mristudio.org</a> and select the first 12 gradients under Siemens DICOM (Lines 0-11).<br>
3. b-Value is 700. And I add the folder of Set 1 to the "DICOM Image-File Folders" section and click OK.<br> 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)<br>
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)<br> 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).<br>
7. I go back to the "Image" tab and save the following files:<br> 7a. Anisotropy-FA --> test.FA<br> 7b. color map 0 --> test.color<br> 7c. eigenvector 0 --> test.vec<br> 7d. tensor images (all 6) --> test.d<br>
7e. dwi file --> test.dwi<br> 7f. b0 file --> test.b0<br> 7g. eigenvalue 0 file --> test.ev0<br><br> 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.<br>
9. I click on the "Color Map" button select both the .fa and .vec files and click OK.<br> 10. I then click on the "Fiber" tab and check off ""show items in 2D image", "roi drawing enable", and "user defined".<br>
11. I proceed to draw an arbitrary ROI in the image in the top-right quadrant. <br> 12. The area selected has 16 fibers (according to statistics button). I click on the save icon next to the "FACT" button.<br>
13. I click on the save icon under the "ROI - Operation" section as well. I save it as the Graphic Compatible (Default) option. <br><br> 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. <br>
<br> 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?<br>
Thank you very much for your time.<br><br> - RJ<br><br> <br>-- <br>- RJ<br>
</div>
</div><br><br clear="all"><br>-- <br>- RJ<br>