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.<div><br></div><div>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.</div>
<div>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.</div>
<div><br></div><div>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:</div>
<div><br></div><div>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? </div>
<div><br></div><div>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?</div>
<div><br></div><div>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) </div>
<div><br></div><div>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? </div>
<div><br></div><div>Many thanks</div><div><br></div><div>Siewmin</div><div><br></div><div><br></div><div><br></div><div><br></div>