3dTRfix time offset information


I want to use 3dTRfix to resample cardiac-gated fMRI data to uniform time intervals. 3dTRfix says resampling will include the effects of slice time offsets if they are stored in input dataset’s header. I believe this is to correct for slice timing difference between slices.
I used custom-made acquisition sequence to collect my data. My question is: which header field does 3dTRfix use for this time offset? I don’t know if it is saved in my header. If it isn’t, perhaps it can modify the header to include it.
I’m new to afni.

Thank you,

Hi Christine,

Okay, I did not even know we had a 3dTRfix program…

Populate the same fields as in a typical NIFTI or AFNI time series dataset (i.e. there is nothing special to do for 3dTRfix). For slice timing there are many fields, but let’s see what you have, first.

What does “3dinfo -slice_timing” say about that dataset?
Or if it is in NIFTI format (call it data.nii) what is the output from:

nifti_tool -disp_hdr -field HDR_SLICE_TIMING_FIELDS -infiles data.nii

If the timing information is not present 3dTcat -tpattern can probably be used to add it.

  • rick