Hi all,
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
Thanks,
Matt
Hi Matt,
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?
and/or
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.
For reference:
Outputs generated from running DIFFPREP are detailed in the following page: https://tortoise.nibib.nih.gov/tortoise/v313/9-outputs-diffprep
Hope this helps,
Thanks,
Amritha