I have a good AC-PC aligned T2star image for each subject that aligns well with the DTI for most subjects, but some DTI alignment with this T2star ACPC image is poor. Are there alignment options within the DIFFPREP command to improve this?
Just to clarify:
1) Does this mean that you are using a T2* (and not a T2w) volume as a reference volume in either DIFFPREP?
2) Are you aligning the T2* to your already-TORTOISE-processed data, and *that* is failing?
3) If you overlay the T2* volume on its unhappy partner DWI in some viewer (like AFNI!), do they overlay at all?
4) If you have AFNI, what is the output of the following command:
3dinfo -o3 -extent -orient -prefix DWI_FILENAME T2_FILENAME
To further investigate the problem, if you are running DIFFPREP with EPI correction switched on, it would be helpful to run the command with the tag --keep_intermediate 1. This will write out all the outputs in the _proc folder and helps to understand the exact step where the processing is failing. My intuition is that the last step of DIFFPREP i.e rigid registration to structural maybe failing.
The main intermediate file of interest would be 'rpd_epi_b0.nii' and 'rpd_epi_structrual.nii'. Please note that these files are not in the structural space yet but infact still in the b0 space. What these files will help understand is if the structural file you are providing is being used correctly by DIFFPREP. If the rpd files look aligned but the DMC.nii and DMC_structrual do not look aligned, then you can confirm that the last rigid step is failing.