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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi RJ,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>The procedure you described seems fine.
You can send me some screen shots to me at <a href="mailto:susumu@mri.jhu.edu">susumu@mri.jhu.edu</a>.
I’m happy to take a look at the result to make sure that your results are
correct. Please draw an ROI on genu, body, or splenium of the corpus callosum.
Also another one at the cerebral peduncle.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>susumu<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b>Raj Jaswal<br>
<b><span style='font-weight:bold'>Sent:</span></b> Thursday, November 06, 2008
5:02 PM<br>
<b><span style='font-weight:bold'>To:</span></b> mristudio-users@mristudio.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Mristudio-users]
Beginning DTIStudio</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>---------- Forwarded
message ----------<br>
From: <b><span style='font-weight:bold'>Raj Jaswal</span></b> <<a
href="mailto:raj.jaswal@gmail.com">raj.jaswal@gmail.com</a>><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>
<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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<o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br clear=all>
<br>
-- <br>
- RJ<o:p></o:p></span></font></p>
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