Inquiry on -stim_times_subtract Option in AFNI After fmriprep Slice Timing Correction

AFNI Message Board
1

Hi everyone,

I have a question regarding the use of AFNI for subsequent data analysis after preprocessing with fmriprep. In fmriprep, I performed slice timing correction.

When using AFNI's 3dDeconvolve to model my data, do I need to set the -stim_times_subtract option equal to TR/2 when creating the matrix with 3dDeconvolve?

Thank you for your assistance!

Shuning

Software Info:

AFNI_24.2.01

fMRIPrep version: 24.0.1

2

Hello,

Yes. Though to be precise, you should be able to verify the exact TR offset to subtract from either the NIFTI file:

nifti_tool -disp_hdr -field toffset -infiles DATASET.nii

or from the JSON file, using the "StartTime" field.

  • rick
1 Like
3

Hi Rick,

Thank you very much for your help! However, I noticed that the start time in the JSON file shows 0.996,
image

but the data obtained using this script you suggested appears to be inconsistent:

image

Could you help clarify this discrepancy?

Thank you!

Shuning

4

It seems most likely that the JSON file is correct and that the creator simply did not duplicate the information in the NIFTI datasets. This aspect of where to put information does make BIDS a bit messy, with a desire not to duplicate information competing against having a dataset or a JSON file being complete.

  • rick