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<p class=MsoNormal><font size=3 color=navy face="Times New Roman"><span
style='font-size:12.0pt;color:navy'>Siewmin raised some important points and I
hope other users could gain some important information from this thread.<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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<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> I got the mean DWI and tensor file from the original 4D DWI. The
tensor file is as you've said, which contains "Dxx, Dyy, Dzz, Dxy,
Dxz Dyz" in one file. In Landmarker, I loaded only the mean DWI of the
subject and then the tensor file with the "open .d" button. The 4D
raw DWI is not used in Landmarker or later. With the "linear" option
in AIR, I could rotate the tensor and the mean DWI to the template DWI without
having to subsample the input data first. The "nonlinear" option requires
the subject data (mean DWI and the tensor file) to be of the same dimension as
the template (i.e 181, 217, 181 if ICBM81 DWI is used as template). This is
noted in the pop up message, and it would only continue once the input files
are resampled to the template. <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'>>It is always advised to do linear transformation
first. To start non-linear, you have to make sure that the brain locations and
shapes are as similar as possible. This is similar to non-linear fitting. You
always have to provide “initial” values close to the real solutions.
Otherwise, non-linear fitting could converge to a wrong solution (trapped by “local
minima”).<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, I tried affine in the linear registration option. The
output DWI of the registration is identical to the input of the DWIs if I used
one of my subject's DWI as the template. Using the 2nd order polynomial in
nonlinear option, an error message occurs "registration terminated due to
a calculation problem, please try a lower order model". It seems to only
work if the template is one of those provided in Landmarker.<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'>> If you can send us two images you are
having the problem, we can take a look at why AIR doesn’t work.<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'>I then saved the rotated tensor file as one file in the .dat format and
the linearly registered 3D meanDWI. In MRIview3D, I loaded this new 3D
DWI and open this new tensor.dat file with the open.dat button to re-calculates
the fa, colour map etc. I viewed the colour map output from this and it looks
pretty good, and as described previously. <font color=navy><span
style='color:navy'><o:p></o:p></span></font></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'>> This is the correct procedure.<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=3 face="Times New Roman"><span style='font-size:
12.0pt'>I saved the fa and principal eigenvector file and used them to perform
fiber-tracking. The tracts that are manually extracted obtained looks similiar
to the fiber tracts from the original raw 4D DWI. <font color=navy><span
style='color:navy'><o:p></o:p></span></font></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'>> That is a good sign.<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=3 face="Times New Roman"><span style='font-size:
12.0pt'>The FA values of these tracts are smaller uniformly in comparison, and
the assymetry preserved (i.e the left tract FA is smaller than the right tract
FA using the maps calculated from the original and rotated tensor). <font
color=navy><span style='color:navy'><o:p></o:p></span></font></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'>> Normalization requires pixel
interpolation, which leads to decreased FA. So you can not compare FA values
with and without normalization.<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=3 face="Times New Roman"><span style='font-size:
12.0pt'>If the non-linear option is used, is there a problem that the tensor is
subsampled first before it is re-oriented, as described above? <font
color=navy><span style='color:navy'><o:p></o:p></span></font></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'>> As I mentioned above, nonlinear
should be AFTER linear transformation. This means, the data are transformed
multiple times and pixels are interpolated multiple times. To avoid this, once
you did linear (save transformation matrix: T-linear) and nonlinear (save
transformation matrix: T-nonlinear), you can combine the T-linear x T-nonlinear
using one of the buttons in the LDDMM section. Once you combined all
transformation matrices, you can apply it only once to the original image in
the native space.<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'>> Another interesting thing is, there
are two ways to transform images; transform your image to an atlas or transform
atlas (usually, binary segmentation map) to your original data for automated
segmentation. For the latter approach, you don’t have to transform
(therefore interpolate) your original data. When you transform the atlas
(segmentation map), make sure to use “nearest neighbor” (no
interpolation), not the tri-linear interpolation. The segmentation map consists
of arbitrary numbers assigned to each segment (e.g. the internal capsule is “1”
and the corona radiata is “3”). If you interpolate these two
segments and obtain “2” in between these two segments and if “2”
means pons, you would get the pons in between the internal capsule and the
corona radiata. On the other hand, when you are transforming your data to an
atlas space, use the tri-linear interpolation. Otherwise, you could get strange
discontinuity artifacts.<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=3 face="Times New Roman"><span style='font-size:
12.0pt'>Do you suggest using the affine or non-linear transformation of
the DWIs and the corresponding transformation of the tensor? Lastly,
I'm not sure if the colour map display is of an issue? It occurs both
using the linear affine option and the non-linear option.<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'>> When everything is working right, the
color map should look smooth and clean. Maybe you are using “nearest
neighbor” for the tensor transformation?<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'>Thanks<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'>Siewmin<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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<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'>On Sat, May 9, 2009 at 7:44 AM, susumu <<a
href="mailto:susumu@mri.jhu.edu" target="_blank">susumu@mri.jhu.edu</a>>
wrote:<o:p></o:p></span></font></p>
<div link=blue vlink=purple>
<div>
<div>
<div>
<p><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>
</div>
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<div>
<p><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><font size=3 color=navy face="Times New Roman"><span style='font-size:12.0pt;
color:navy'> </span></font><o:p></o:p></p>
</div>
<p><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).</span></font><o:p></o:p></p>
<p><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.</span></font><o:p></o:p></p>
<p><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.</span></font><o:p></o:p></p>
<p><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".</span></font><o:p></o:p></p>
<p><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.</span></font><o:p></o:p></p>
<p><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).</span></font><o:p></o:p></p>
</div>
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<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
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<div>
<p><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><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
<p><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.</span></font><o:p></o:p></p>
</div>
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<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
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<div>
<p><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><font size=3 color=navy face="Times New Roman"><span style='font-size:12.0pt;
color:navy'> </span></font><o:p></o:p></p>
</div>
<p><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..</span></font><o:p></o:p></p>
<p><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.</span></font><o:p></o:p></p>
</div>
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<p><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><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><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
<p><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??</span></font><o:p></o:p></p>
<p><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.</span></font><o:p></o:p></p>
</div>
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<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
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<div>
<p><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><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
<p><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. </span></font><o:p></o:p></p>
<p><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;</span></font><o:p></o:p></p>
<p><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</span></font><o:p></o:p></p>
<p><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</span></font><o:p></o:p></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
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<div>
<p><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><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
<p><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?</span></font><o:p></o:p></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p><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>
</div>
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<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
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<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
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