[Mristudio-users] Gradient Table for Philips

[Dresner, Alex]

Dear Andrew,
Dr. Mori's message was more complete than mine was, so I've copied his response below.  In your .par file, you are correct that those three columns are your diffusion directions.  And though it says there are 33 directions, the last direction is 0.00, 0.00, 0.00 for the calculated DWI which should be replaced with 100, 100, 100 in your table for DTI Studio.  And the direction before that (next-to-last in the .par file) is the b0 image, because it is labeled with direction 0.00, 0.00, 0.00 and b-value = 1 (the column to the left of the gradient number, so those lines read ... 1 33 0 0 0.000 0.000 0.000 ...).

As far as checking the results to see if you have entered the correct gradient table, there's no specific method.  The easiest thing to do is to compare the FA color map to that of the sample dataset and check obvious structures like the corpus callosum (should be red) and the optical fibers (should be green).  Again I will quote Professor Mori: (DTI Studio mailing list, 6/10/10)
There are several ways to notice wrong gradient tables;

1) Totally wrong table: If the table is totally wrong, the color map doesn't make sense. So check color map first.
2) X/Y/Z permutation: If X/Y/Z is miss signed, the color of the color maps doesn't look right. For example, the corpus callosum should look red, not green
3) +/- sign error: Perform tractography. If sign is wrong, it doesn't make any sense.
4) More subtle errors: Look at fitting residual (error) map. There is a file called "DtiStudioUpdate.doc" at https://www.mristudio.org/wiki/changelog/dtistudio-3.0.2. This explains how to get the fitting error maps.
5) Oblique angle: The attached file explains in detail. To make sure everything is right, you can scan a person twice. One in a regular position and one in severe oblique. If everything is working, you should get anatomically comparable tractography results.

Regards,
Alex

Dear Alex,

Thank you very much for your prompt response.

 The attached is my .par file. Do you mean that  the "#  diffusion (ap, fh, rl)     (3*float)" , for example  -0.001   -0.076   -0.997, is a diffusion direction? Since there are 33 directions in my .PAR file and are labeled from 1 to 33, should I change their label to 0,1,..32?  In addition , should I add a extra line (33) with 100, 100, 100 in the end of the gradient table?

By the way, is there any way based on the result I can check whether I use the right gradient table?

Again, thank you for your time and help!

Chunxiao(Andrew)


From: mristudio-users-bounces at mristudio.org [mailto:mristudio-users-bounces at mristudio.org] On Behalf Of susumu mori
Sent: Wednesday, November 24, 2010 6:27 AM
To: DTI Studio, ROI Editor, DiffeoMap Questions/Support
Subject: Re: [Mristudio-users] Gradient Table for Philips

1) Please read your REC file using Mri3DView. Use the image dimensions you get from the PAR file.
2) After the images are read, please go through the images using the pull-down menu in the right column of the viewing window. Check if all the images (b0 and DWIs) look fine.
3) Find out how many 3D images are loaded. If you used Philips "High" gradient orientation, you should have 34 images loaded; one b0, 32 DWIs, and one calculated DWIs (I think this is the sum of all DWIs).
4) Make sure where is b0. It could be the first or the second from the last. The calculated DWI is always at the end.
5) Close the window and start DtiMapping.
6) Cut&Paste your gradient table to the appropriate section. You have to make sure several things here;
a: The position of b0; First or the second from the last
b: The number of rows; It has to be 34. Sometimes you find a table with only 33 lines ignoring the last calculated image. In this case, you get the error message, complaining that the file size doesn't match. Because the last image is not used anyway, you can ignore the message and proceed. The last image is thrown away. Or, you can increase the number of row to 34 by adding 33: 100, 100, 100, in which [100, 100, 100] send the message to DtiStudio to remove this image.
c: Please make sure if you used "gradient overplus ON" or "OFF", because you have to use different tables.
7) If you still get the file size error message, something is wrong.
On Tue, Nov 23, 2010 at 5:21 PM, Dresner, Alex <alex.dresner at philips.com<mailto:alex.dresner at philips.com>> wrote:
Dear Chunxiao,
Your gradient table is also in the .PAR file.  You should be able to read the .PAR file with any text reader such as WordPad, NotePad or Word; lower in the file is a table of parameters per-image.  On the right-hand-side of that table are the diffusion directions in three columns.
Regards,
Alex
____________________
M. Alex Dresner, Ph.D.
MR Clinical Scientist
alex.dresner at philips.com<mailto:alex.dresner at philips.com>
____________________
From: mristudio-users-bounces at mristudio.org<mailto:mristudio-users-bounces at mristudio.org> [mailto:mristudio-users-bounces at mristudio.org<mailto:mristudio-users-bounces at mristudio.org>] On Behalf Of Chunxiao Zhou
Sent: Tuesday, November 23, 2010 5:07 PM
To: mristudio-users at mristudio.org<mailto:mristudio-users at mristudio.org>
Subject: [Mristudio-users] Gradient Table for Philips

Hello,
When I do tensor calculation for my own data , there is a warning message "File size is bigger than DW-image size, continue anyway?". I get all image size parameters from my .par file ( I use Philip .REC .PAR data). I guess the reason is that I use the default ParRec gradient table from your GradientTable file. How could I get my gradient table from my file?
Thank you.
Chunxiao(Andrew)
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