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History of AFNI updates  

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May 20, 2022 01:42PM
Hi Megan,

There are just a few things to note here, and the main one is that 1D (TSV) inputs should be concatenated across runs.

For example, the 4 sub-1055_task-learn_run-*_motion.tsv should be concatenated, with only the 1 input passed via -regress_motion_file. I _could_ consider allowing 1 per run as an alternative, but it is not an option right now.

Also, -regress_extra_ortvec can take multiple files as input, but they should also be concatenated across runs. So if you were to :
cat sub-1055_task-learn_run-*_aCompCor6.tsv > ortvec_rall_aCompCor6.1D
(and similarly for cosine and fd), then the options might read:

-regress_extra_ortvec ortvec_rall_aCompCor6.1D   \
                      ortvec_rall_cosine.1D      \
                      ortvec_rall_fd.1D          \
-regress_extra_ortvec_labels aCompcor6 cosine fd \

Note that the "labels" option just names the ortvec files in some way.


Also, the -regress_stim_times_offset parameter is probably negated. If fmriprep has done 3dTshift to align to the middle(ish) of the TR, then it will be as if the EPI timing is later than the start of the TR, and so relatively, the task timing should be earlier. Consider using:

-regress_stim_times_offset -0.870967741935484

Also, just to make it easier, since the -regress_stim_types and -regress_basis_multi parameters are all the same, it is okay to use a single parameter, as in:
-regress_stim_types AM1           \
-regress_basis_multi 'dmBLOCK(0)' \

Does that seem reasonable?

- rick
Subject Author Posted

afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 19, 2022 02:05PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

rick reynolds May 20, 2022 01:42PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 23, 2022 08:26AM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 27, 2022 11:45AM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

rick reynolds May 27, 2022 01:04PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 27, 2022 04:11PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

rick reynolds May 27, 2022 07:44PM

Re: afniproc.py error -regress_motion_per_run follows unknown arg

MeganQ May 30, 2022 08:28AM



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