Hello,
We are trying to preprocess a resting-state fMRI dataset that was obtained using a multiband (factor of 4) EPI sequence. Would you happen to have an example afni_proc.py script that I can take a look at, to learn how I should modify our tshift block? Some of the data set has been exported in Philips PAR/REC format, so it may not be possible to recover this information directly from the header.
Sincerely,
Ann
Hi Ann,
Do you have the slice times themselves? What's the overall TR?
If you have the slice timing in a text file, you can specify it in afni_proc with:
-tshift_opts_ts -tpattern @filename
If you have a BIDS sidecar, you can use
abids_tool.py -add_slice_times -input my_bids_fmri.nii.gz
to automatically insert the slice time info from the json before afni_proc is run and it'll find the slice times in the header of the files.
-PM
Hello Peter,
Yes, we have the slice times themselves as well as the TR information. I totally missed that you can read in the timing from the text file! Many thanks for the info.
Sincerely,
Ann
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