- usage: /home/afniHQ/afni.build/pub.dist/bin/linux_ubuntu_16_64/abids_tool.py
-input DSET [DSET …] [-help] (-TR_match | -add_TR | -add_slice_times | -copy PREFIX [PREFIX …])
This program does various things with BIDS formatted datasets created with dcm2niix_afni or dcm2niix. The main point as of now is to pull information from the matching json file and 3drefit the input dataset. If you just want info from the matching json file, use abids_json_info.py.
This assumes that the nifti dataset was converted from dicoms using dcm2niix_afni or dcm2niix with the -b (BIDS) option. So a json file and matching dataset in NIFTI format should be present. (NO AFNI FORMAT...) The json file should end in .json (lower case) as outputted from dcm2niix. The program will try to find a json file that matches the prefix of the input dataset. Like this: my_bids_fmri.nii.gz <-> my_bids_fmri.json For most options, 3drefit will be run on the -input dataset(s). So the dataset(s) will be overwritten!! Make sure you want to do this!! All of the caveates for 3drefit apply here...!! (https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/3drefit_sphx.html) For example, when using -add_TR, if the dataset has slice time offsets, these will be scaled by the factor newTR/oldTR. So you may want to use -add_TR BEFORE -add_slice_times. However, afni_dcm2niix usually adds the correct TR to the dataset header automatically. So you should not need -add_TR... Also, this has only been tested with 3d+time fMRI data acquired in the axial (z or k) direction. If you have problems with data acquired in the sagittal or coronal direction, post to the message board.
abids_tool.py -add_slice_times -input my_bids_fmri.nii.gz
Required arguments: -input DSET [DSET ...] At least one 3d+time dataset. Only one of these: -TR_match Check if the TR in the json file matches the TR from input dataset header. (1 if match) -add_TR Add the TR from the BIDS json file to the input dataset using 3drefit. -add_slice_times Add the slice times from the BIDS json file to the input dataset using 3drefit. -copy PREFIX [PREFIX ...] Copy both the NIFTI dataset(s) AND matching .json file(s) to PREFIX. Must have the same number of prefixes as datasets! Optional arguments: -help Show this help and exit. Justin Rajendra circa 05/2018 For Wolverine, hiya Bub... Keep on keeping on!