I am trying to use TORTOISE to susceptibility-induced distortion correction on my DTI and I've selected the option ANTSSyN, However, in the log files, I am not seeing a nonlinear registration file, or even an affine registration file. I also don't see a reference to a nonlinear registration in the console window. Moreover, I see some areas where the deformation is not quite working. Am I missing something?
When I do this manually, using ANTs, I get a nifti Warp file and a "GenericAffine.mat" file, and I get almost perfect distortion correction (apart from areas of signal loss).
My DIFFPREP call is:
DIFFPREP --dwi ap.nii --bvecs ap_rvec.dat --bvals ap_bval.dat --structural t2w_resamp.nii.gz --phase vertical --will_be_drbuddied 0 --reg_settings TORTOISE_AFNI_bootcamp_DATA_registration_settings.dmc -e ANTSSyN --mask_image ../nodif_brain_mask.nii.gz --do_QC --center_of_mass
Sorry the correction is not working. The command looks correct. What are the outputs generated when you run the command?
I can offer two solutions:
1) Please take a look at your T2 structural used in the correction w.r.t to original b0 of your image. Do the images look flipped w.r.t to each other?
2) try importing the data into TORTOISE using ImportNIFTI command and then run DIFFPREP using the .list file. Not sure if this will help but worth a try.
Outputs generated from running DIFFPREP are detailed in the following page: https://tortoise.nibib.nih.gov/tortoise/v313/9-outputs-diffprep
Hope this helps,