[Mristudio-users] transformations with AIR in Landmarker

[Siewmin Gan]

Hi, I am trying to perform tractography analysis on AC-PC aligned data with
and without rotating the tensor, and came across some questions on the way,
mainly with regards to the transformation steps.
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.

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:

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?

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?

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)

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?

Many thanks

Siewmin
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