I have some subject level FSL data (parameter estimate NIFTI files) that I would like to convert/transform into TLRC (TT_N27) space so that I can compare these FSL data with other data generated through AFNI.
I have followed these steps:
1) Deoblique the FSL pe#.nii.gz files using 3dWarp with the -deoblique flag.
2) Generate tlrc space using 3drefit -view
3) Align to standard brain using @Align_Centers -base /home/ghindy/abin/TT_N27+tlrc
To check if this worked, I overlay the transformed and aligned PE file on the anat file generated by AFNI. As is clear from the screenshot, the mask is crooked and too large:
[
dl.dropboxusercontent.com]
If I omit the deobliqueing stage (1), the result looks better but still too large:
[
dl.dropboxusercontent.com]
If there a better way to get FSL pe.nii.gz files to come into standard TLRC space for comparison to AFNI output?
