hello-

i am wondering if there was any progress/updates to this post- i used fsl (flirt) to do intermodal registration (one image from a EPI timeseries to high res anat) from which i obtained a fsl .mat file (4 x 4 matrix) as the first step in my pipeline. i then did all of my pre-processing and level one analyses on the unregistered timeseries, with the idea that i could just apply the transformation matrix to the psc change files prior to stereotaxic normalization for level two analyses. when i applied the transformation matrix to the psc files (again using flirt and the .mat file from the original registration) it worked beautifully (ie good spatial alignment with the t1) with the exception that all of the psc values were now changed. i tried to see if this was due to the application of some scalar but it was not immediately evident to me that this was the case (not sure if i was looking in the right places or if things were changed due to the interpolation or something else). the range of values (stored as floats) changed from -4.53... to 6.89... in the psc file prior to the application of the transformation matrix via flirt to -.0008... to .00127... following the transformation.

my questions- can 3dWarp or 3drotate or some other program read in the 4x4 matrix from fsl and do the appropriate transformation. i did not see an option and when i tried using the -fsl_matvec file with 3dwarp the data were still misaligned. this would be wonderbar if it existed.

if not, is there another program like cat_matvec that can be used to transform the fsl matrix into something that afni can use.

either one would be greatly appreciated prior to the afni intermodal registration program. thanks

andy