Preprocesing of multiband data

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1

Hello AFNI experts,

I want to preprocess my data in native space using AFNI to generate the connectivity maps.

My dataset has the following parameters:
TR = 0.681ms, and Time Points = 870, slice thickness is 2.5mm
I used the following command:

afni_proc.py -subj_id MCSA1_notlrc.rest -dsets BS0001MC_RSN.nii -copy_anat BS0001MC_t1.nii -blocks despike tshift align volreg blur mask regress -tcat_remove_first_trs 3 -tshift_interp -Fourier -blur_size 3 -regress_motion_per_run -volreg_align_e2a -regress_anaticor -regress_censor_motion 0.5 -regress_censor_outliers 0.1 -regress_bandpass 0.005 0.05 -regress_apply_mot_types demean deriv -regress_run_clustsim yes -regress_est_blur_epits -regress_est_blur_errts

Unfortunately, I can not understand the output

Please help me to choose the correct input file for the 3dNetCorr from the afni_proc.py output

Whenever I try to overlay the output file on skull-stripped anat data I see the message to perform the following command
3dwarp -deoblique

Please help me to understand and rectify these errors.

Thank you.

2

Sorry for being slow…

The obliquity warnings are essentially just reminders
that the data is not cardinal. Whether you care depends
on what you do with the data. The coordinates shown in
the afni GUI are not quite accurate when oblique.

If you ran 3dWarp on just the anat before runnning
afni_proc.py, I think the EPI data would not be oblique
at the end.

The output from afni_proc.py will be an errts dataset in
this case, since there are no task betas that you want.
The datasets should be called something like:

errts*.anaticor*

Does that seem reasonable?

  • rick