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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>First, I tried rotating the tensor but had problems with the results.
When I look at the colour map from the resulting tensor, it looks ok generally,
but there are certain areas of blotchiness and some mixing of colours
especially in the sidelines of white matter regions (i.e there can be a
striking red line or a blotch of redness in the middle of a green regions
within the saggital stratum). These are the steps I took, and would like to
check if it is done correctly.<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'>1. resample mean DWI of subject data (together with the 4D DTI data and
the tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order
trilinear) the resampled meandwi of subject to dwi of template, and used that
to drive the transformation of the resampled 4D DTI and the resampled tensor
simultaneously. (The resampled tensor was loaded with the .dat button.) I used
MRIview 3D to load the normalised 4D DTI, followed by the normalised tensor
with the .dat button, and calculate the fa, colour etc maps from the normalised
tensor. I tried various thresholding with AIR but the colour maps problem
remains.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;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'>> First of all, I think you don't have
to resample DTI images before AIR. AIR can take data with different matrix and
pixel sizes and the output images have the same matrix/pixel dimensions as the
template (in your case, 181x217x181 of ICBM81).<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'>> By saying "4D DTI", do you
mean raw 4D DWI before tensor calculation? if so, I don't think you want
transform raw DWIs. If you want to do anything to raw DTI, you also want to
transform the corresponding gradient table, which could be messy. Our tools do
not provide methods to transform raw DWIs.<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'>> When you say, "tensor"
data, I assume you are talking about 4D file that contains "Dxx, Dyy, Dzz,
Dxy, Dxz, Dyz" images in one file. If so, please make sure that you load
this 4D tensor file by the "open .d" button in Landmarker. Once read
in Landmarker, the 4D tensor file is disassembled to 6 3D data for Dxx, Dyy,
Dzz, Dxy, Dxz, Dyz.<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'>> Once the AIR is done using mean DWI
(your data) - mean DWI (template), the 6 3D tensor element data should be
stored all together into one file as a "transformed 4D tensor file".<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'>> This transformed 4D tensor file needs
to be read into DtiStudio to re-calculate new transformed FA, color, vec, etc.<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 blotch-looking colormap could happen
by; 1) transform the color map directly (you should recreate color maps using
the recalcuated FA and vector files from the transformed tensor file or 2) you
transformed a vector file (transformed vector files should be obtained from the
transformed tensor file. Vector can not be directly transformed).<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'><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'>Second, I tried without rotating the tensor. I calculate the scalar and
colour maps from the original 4D DTI data, aligned the maps to AC-PC line, draw
rois on them and invert transform the rois back to native dti space to extract
the relevant white matter tracts. I had two problems here. 1) with
orienting the subjects scalar DWI to another particular subject's DWI
with rigid transformation in AIR and 2) Invert transform ROIs drawn on the
registered colour map back to the original DTI space. These are the steps I
took:<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'>> Maybe you are transforming raw DWI
data? Again, you should not transform raw DWI and recalcuate tensor. You have
to first calculate tensor (throw away the raw DWIs) and transform the tensor.<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'><o:p> </o:p></span></font></p>
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<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>1. A subject's data which is acquired // to AC-PC is chosen and other
subjects not acquired //to AC are registered to this. Again the meanDWI is used
for source and target images, this time using rigid transformation in AIR in
Landmarker. However, there is no difference detected after the transformation
has taken place. However, if I change the target image from a subject's DWI to
the mean DWI of the ICBM 81 template, it works but the source data would be
subsampled to that of the ICBM template. I'm not sure why it didn't work in the
1st case? <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;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'>> As mentioned above, AIR not only
adjust the image orientation and translation, but also the matrix / pixel
size..<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'>> Rigid transformation of AIR is
sometimes very cranky. We are working on alternative methods now. please try
different threshold or affine.<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'><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'>Additionally, using either another subject or the template DWI as
target image, would yield the an output file (AlignlinearOutput.air) when the
transformation has been performed, which I saved the
invert_AlignlinearOutput.air. However, when I clicked on these .air files in
the folder it is saved as an installer package, I get the following error
message " An error has occurred.The application could not be
installed because the AIR file is damaged. Try obtaining a new AIR file from
the application author." I have installed the air application and placed
it in the same folder, together with the alignlinear.exe file. Is it possible
to view the transformation matrix files saved or did I not installed the air
application appropriately?<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'>> Maybe Xin can answer this question
better, but I'm not sure why you want to open *.air??<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'>> Once you save the *.air, you can load
it back to Landmarker and apply to images by using the "open M"
button in the LDDMM section.<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'><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'>2. ROIs are drawn on the transformed AC-PC aligned colour maps
with ROI-editor. I would like to check if it's OK to draw rois on the
transformed colour map? These ROIs would later be used as the start ROI
and stop ROI to extract the corresponding white matter tract with DTI
studio) <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'>> Drawing ROIs on color maps is fine.
ROI is simply 1/0 information about which pixels you chose and the color maps
are simply what is displayed to aid your ROI drawing. <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'>> If you draw ROI in the atlas space
and have a plan to back-transform your ROI files to the native space, there are
several things you have to know;<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'>1) Atlas space is 1x1x1 and your native
space could be 2-3 mm. The ROI defined in the thin 1 mm slice could be lost
after transformation to the thick 2-3mm slice. Therefore, you have to create 3D
ROIs in the atlas space with at least 3mm thick<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'>2) Use nearest neighbor interpolation when
you back-transfer. You don't want to get a pixel with 0.3 or 0.4 after
transformation. You want 1/0<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'><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'>3. I tried to invert-transform these ROIs back to the original
DTI space with the previously saved invert_matrix.air file. How is that done in
Landmarker and if the previous error message needs to be resolved before I can
used the matrix files? <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'>> Xin, how to do the
invert-transformation of *.air?<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'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Susumu</span></font><o:p></o:p></p>
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<p class=MsoNormal><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><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><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><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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