AFNI version info (afni -ver): AFNI_24.3.08 Elagabalus
Hi AFNI community,
I have an issue about the slice timing when switching from BIDS to AFNI data type.
I am working with a resting state fMRI dataset that was given to me already in BIDS format. Looking at the bold series of the dataset, there is for example:
sub-02.func.nii.gz
sub-02.func.json
Where the .json sidecar holds some parameters of the acquisition, like the SliceTiming (in this case, 70 slice times for the 70 axial slices direction with alt+z2 encoding).
This info is not included in the .nii file, and if I try to visualize it in the AFNI GUI, all the slices and voxels of the same subbrick are equal time (multiples of TR that is 3 s, so like 0,3,6 etc).
So, to be able to process it in AFNI, I tried to add the slice timing in the dataset with:
abids_tool.py -add_slice_times -input sub-02.func.nii.gz
However, although the output of the script seems to be all good (see bottom), I am confused of what happened to the .nii dataset...
Because the header now includes the slice timings, but if I try to verify the timings with the AFNI GUI, nothing changed: also now, every volume is all same time as before in every voxel and every slice. Is this expected?
Moreover, I don't know if this is related, but I tried to ignore this fact and go on with an afni proc py script, and it ended with a 3dREMLfit error compaining about high singular value and strong collinearity in the X matrix.
This was the output of the abids_tool.py execution:
3drefit -Tslices 1.508 0.0 1.55 0.043 1.592 0.087 1.635 0.13 1.677 0.173 1.722 0.215 1.765 0.26 1.808 0.302 1.85 0.345 1.893 0.388 1.938 0.43 1.98 0.475 2.022 0.518 2.065 0.56 2.11 0.603 2.152 0.645 2.195 0.69 2.238 0.733 2.28 0.775 2.325 0.818 2.367 0.86 2.41 0.905 2.453 0.948 2.495 0.99 2.54 1.032 2.583 1.075 2.625 1.12 2.668 1.163 2.71 1.205 2.755 1.248 2.798 1.293 2.84 1.335 2.883 1.378 2.925 1.42 2.97 1.462 sub-02.func.nii.gz
++ 3drefit: AFNI version=AFNI_24.3.08 (Dec 6 2024) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset sub-02.func.nii.gz
+ setting slice time offsets
+ loading and re-writing dataset sub-02.func.nii.gz (sub-02.func.nii.gz in NIFTI storage)
++ 3drefit processed 1 datasets
Added slice times:
1.508 0.0 1.55 0.043 1.592 0.087 1.635 0.13 1.677 0.173 1.722 0.215 1.765 0.26 1.808 0.302 1.85 0.345 1.893 0.388 1.938 0.43 1.98 0.475 2.022 0.518 2.065 0.56 2.11 0.603 2.152 0.645 2.195 0.69 2.238 0.733 2.28 0.775 2.325 0.818 2.367 0.86 2.41 0.905 2.453 0.948 2.495 0.99 2.54 1.032 2.583 1.075 2.625 1.12 2.668 1.163 2.71 1.205 2.755 1.248 2.798 1.293 2.84 1.335 2.883 1.378 2.925 1.42 2.97 1.462
to sub-02.func.nii.gz.
Any help would be appreciated <3
Many thanks,
Ms