[Mristudio-users] transformations with AIR in Landmarker

[Siewmin Gan]

Hi Susumu, Thanks.
 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.

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.
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. 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. 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). 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?
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.

Thanks

Siewmin




On Sat, May 9, 2009 at 7:44 AM, susumu <susumu at mri.jhu.edu> wrote:

>   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.
>
> 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.
>
>
>
> > 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).
>
> > 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.
>
> > 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.
>
> > 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".
>
> > This transformed 4D tensor file needs to be read into DtiStudio to
> re-calculate new transformed FA, color, vec, etc.
>
> > 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).
>
>
>
> 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:
>
>
>
> > 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.
>
>
>
> 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?
>
>
>
> > As mentioned above, AIR not only adjust the image orientation and
> translation, but also the matrix / pixel size..
>
> > Rigid transformation of AIR is sometimes very cranky. We are working on
> alternative methods now. please try different threshold or affine.
>
>
>
> 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?
>
>
>
> > Maybe Xin can answer this question better, but I'm not sure why you want
> to open *.air??
>
> > 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.
>
>
>
> 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)
>
>
>
> > 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.
>
> > 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;
>
> 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
>
> 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
>
>
>
> 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?
>
>
>
> > Xin, how to do the invert-transformation of *.air?
>
>
>
> Susumu
>
>
>
>
>
>
>
>
>
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