afni.nimh.nih.gov

Hey,

I'm trying running distortion correction on an oblique functional dataset of 54 slices through Matlab 2019a.
Everything seemed to work until I found out some black spots on the undistorted data.

These are the commands I use - and please find attached an example picture of the problem

- to convert dicom in afni readable nifti
dcm_to_nii_command = sprintf("Dimon -infile_prefix '%s/*.dcm' -use_obl_origin -gert_create_dataset -gert_write_as_nifti -gert_outdir %s -gert_to3d_prefix %s", input_directory_path, ...
output_filepath, ...
output_filename);

- to perform the distortion correction
warp_command = sprintf("3dQwarp -plusminus -pmNames reverse forward -source %s -base %s -prefix %s_warp.nii", inv_sbref_path, ...
sbref_path, ...
bids_id);
system(warp_command);

mb_appy_warp_command = sprintf("3dNwarpApply -quintic -nwarp %s_warp_forward_WARP.nii -source %s -prefix %s", bids_id, ...
mb_path, ...
corrected_mb_outpath);
system(mb_appy_warp_command);

sbref_apply_warp_command = sprintf("3dNwarpApply -quintic -nwarp %s_warp_forward_WARP.nii -source %s -prefix %s", bids_id, ...
sbref_path, ...
system(sbref_apply_warp_command);

So when I run this it suggests me to consider to3D -ushort2float. I tried but it seems I'm not allow to do it, and the commans is just ignored.
Any help?

Thanks
Cecilia