Yes, <br><br>There are three cases when things can go wrong even if the colormaps look fine.<br><br>1) Simple mistake in the gradient table (e.g. [1, -1, 0] instead of [1, 1, 0] in one of the tables).<br><br>Here I assume you made a mistake in one or several lines of the gradient table by typos. This is the most difficult kind of problems to catch.<br>
<br>When you do tensor calculation, it asks "Automated Rejection?". This function is not working well in the current implementation. We are about to release a much better version soon, but there is one handy function, called "Create images of the DWI-Fitting" and "Create images of the difference between ....". Click these two check boxes. For outlier rejection threshold, put a large number to effectively turn off this function. After calculation, click "Original-Mean-ADC-STD" button. Here, you can find raw DWI, theoretical DWI back-calculated from fitting results, and difference of the two. Think these results in this way; suppose you have 4 points in a X-Y plot and did a linear fitting. After fitting, you can measure error between the fitting results and each measured point. The bottom row of the inspection window shows the difference (error) maps. These error maps should look random noise. If there is any mistake in the gradient table, you can immediately tell because you can clearly see anatomical structures in this error map. Also, these error maps are handy to visually see the amount of eddy current and subject motion.<br>
<br>2) Oblique angle<br><br>When you are using oblique angle axial imaging AND<br>> you are using Philips scanner AND using the "gradient overplus" option.<br>> you are using Siemens scanner AND the operating system prior to VB15<br>
<br>Then you need to re-calculate your gradient table based on the oblique angles. If you are a Philips scanner user, you can get a handy software from <a href="http://mri.kennedykrieger.org">mri.kennedykrieger.org</a> that can do the calculation. If you are using DICOM, you can simply click "rotate gradient if applicable" beneath the gradient table input section. Then the software can read the oblique info from the header and do the recalculation<br>
<br>3) +/- sign<br><br>If +/- sign is wrong for only one of the table lines, it is the case described in #1. If +/- sign of, for example, all X components of all lines are flipped, that's a totally different story. There is a detailed description of this issue in the manual of DtiStudio. Basically, +/- definition of any given gradient table is arbitrary, and dynamically changed depending on imaging protocol. If +/- signs of one of the X, Y, Z components are flipped, you won't notice by looking at eigenvalue-based maps such as MD and FA. The color map also looks correct. You notice the problem only when you start fiber tracking. Please refer to the manual for detail.<br>
<br><br>Susumu<br><br><div class="gmail_quote">On Sun, Sep 27, 2009 at 1:31 PM, <span dir="ltr"><<a href="mailto:miguel.burgaleta@uam.es">miguel.burgaleta@uam.es</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
Hi Susumu,<br>
<br>
I'm sorry but what I was trying to mean is if I can trust the gradient table whose values come from the DICOM headers.<br>
<br>
I have 2 gradient tables: one from the manufacturer (medium GE) and one from the DICOM headers. When I use the former I get wrong colormaps (I have validated this with other software), but when I use<br>
the latter, the colormaps *seem* to be OK (red corpus callosum, symmetric colors).<br>
<br>
So the question is: even if the CC is solid red and the colormap is symmetric, is it still possible that the gradient table is wrong? Since I am a beginner I am not able to see it just by looking at the colormap.<br>
<br>
I know this is a basic question, perhaps beyond the scope of this list. So any help will be highly appreciated.<br>
<br>
Thanks,<br>
Miguel<div><div></div><div class="h5"><br>
<br>
<br>
Quoting susumu mori <<a href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>>:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Miguel,<br>
<br>
There are two possibilities;<br>
<br>
1) your table is wrong.<br>
2) your table format is wrong.<br>
<br>
I suspect #2. The table has to be rewritten to DtiStudio format, which is;<br>
<br>
0: x, y, z<br>
1: x, y, z<br>
<br>
Common mistakes are;<br>
<br>
0; x, y, z (";" instead of ":")<br>
1: x y z (missing ",")<br>
.<br>
.<br>
(there is no [0, 0, 0] in the table)<br>
<br>
When you have a long table, it is sometimes difficult to catch one mistake.<br>
In this case, please do the following;<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Use your current table and load the images. You will get the problem you<br>
</blockquote>
reported.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Close the window and choose "DtiMapping" again.<br>
You will get the initial data input window, which still remembers all the<br>
</blockquote>
parameters you specified last time, including the gradient table.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Closely inspect the gradient table. This time it contains the table which<br>
</blockquote>
is NOT the one you typed in but the version interpreted by the software. If<br>
you made a mistake in the syntax, it is much easier to catch it in this<br>
version.<br>
<br>
I hope this will help.<br>
<br>
Susumu<br>
<br>
On Fri, Sep 25, 2009 at 7:07 PM, <<a href="mailto:miguel.burgaleta@uam.es" target="_blank">miguel.burgaleta@uam.es</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Dear DTIStudio group,<br>
<br>
I have a beginner's question regarding the gradient table that I<br>
should use with my DTI. The scanner is a GE and I already have the<br>
standard medium table from the manufacturer, but I get weird FA<br>
colormaps when using it (non-symmetric, corpus callosum not red).<br>
However, if I use a gradient table made by reading the DICOM headers<br>
with dcm2nii, I get a gradient table that leads to symmetric, solid<br>
red CC FA colormaps.<br>
<br>
I have read in this list before that this is a good criterion to make<br>
sure that the gradient table is the right one, but also heard that it<br>
could be incorrect too! So the question is how to make sure that the<br>
gradient table is the right one?<br>
<br>
I appreciate your help.<br>
<br>
Miguel<br>
<br>
<br>
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