[Mristudio-users] Gradient Table for Philips

Sat Dec 4 22:12:50 EST 2010

Susumu,

Thank you very much for your update.

Chunxiao(Andrew)

On Sat, Dec 4, 2010 at 3:13 AM, susumu mori <susumu at mri.jhu.edu> wrote:
> Hi Chunxiao and Alex,
> I would be cautious about using the gradient information in PAR file if you
> are using oblique-angle imaging.
> For example, suppose you apply [1, 0, 0] gradient, which is along X (right -
> left). If you rotate the FOV about the Z axes, there are two ways to deliver
> [1, 0, 0]. In the first option, regardless of the rotation angle, the [1, 0,
> 0] is always the physical gradient X. In the second option, [1, 0, 0]
> rotates with FOV such that [1, 0, 0] gradient is always along the X axis of
> the image, meaning the combination of physical X and Y gradients (e.g. [0.9,
> 0.4, 0]).
> Unless you are using "Overplus = on", the gradient table
> is automatically rotated to make sure [1, 0, 0] always means the X axis of
> the image, not the physical gradient. In this case, if the first line of the
> "vendor-supplied" table is [1, 0, 0], you can use the information as is. The
> problem is, if you read the gradient table from PAR file, I am not sure if
> it is stored in the image axes ([1, 0, 0]) or physical axes ([0.9, 0.4. 0]).
> If the latter is the case, you can't use the information as is.
> I wonder if Jonathan or Bennett know the detail of the PAR file gradient
> table.
> Susumu
>
> On Thu, Dec 2, 2010 at 12:54 PM, Dresner, Alex <alex.dresner at philips.com>
> wrote:
>>
>> 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>
>> 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
>>
>> ____________________
>>
>> From: 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
>> 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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