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May 12, 2022 07:14AM
Hi there!

I've been using the same lovely AFNI pipeline to pre-process the various datasets that I'm working on.

We've recently started a new study where we'll be collecting field maps in the hope of doing distortion correction and improving the quality of our data.
I was wondering how exactly I could integrate field maps into the pipeline without breaking something.

The command(s) I'm using to generate the script is as follows:
module load afni/21.1.07
module load anaconda/3.8
module load tedana/0.0.11

afni_proc.py -blocks despike tshift align tlrc volreg mask combine blur scale regress -copy_anat t1.nii.gz -anat_has_skull yes -dsets_me_echo fmri_e1.nii.gz -dsets_me_echo fmri_e2.nii.gz -dsets_me_echo fmri_e3.nii.gz -dsets_me_echo fmri_e4.nii.gz -echo_times 12.9 28.9 44.9 60.9 -reg_echo 2 -tcat_remove_first_trs 10 -align_opts_aea -cost nmi -check_flip -skullstrip_opts -push_to_edge -tlrc_base MNI152_T1_2009c+tlrc -tlrc_NL_warp -volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -mask_epi_anat yes -mask_segment_anat yes -mask_segment_erode yes -combine_method tedana -blur_size 6 -blur_in_mask yes -regress_bandpass 0.01 0.1 -regress_ROI WMe CSF -regress_motion_per_run -regress_censor_motion 3.0 -regress_censor_outliers 0.05 -regress_apply_mot_types demean deriv -regress_est_blur_epits -html_review_style pythonic

In the combine block code, I remove the tedana wrapper bit and add this instead:
tedana -d pb03.SUBJ.r01.e01.volreg+tlrc.BRIK \
pb03.SUBJ.r01.e02.volreg+tlrc.BRIK \
pb03.SUBJ.r01.e03.volreg+tlrc.BRIK \
pb03.SUBJ.r01.e04.volreg+tlrc.BRIK \
-e 12.9 28.9 44.9 60.9 --mask mask_epi_anat.SUBJ+tlrc.BRIK --debug

Finally, I change the 3dcopy bit to:
3dcopy desc-optcomDenoised_bold.nii.gz pb04.$subj.r$run.combine+orig

I've got a field map (in radians), which has been unwrapped.
[afni.nimh.nih.gov] seems like the thing I should be using but [afni.nimh.nih.gov] is the thing that is used in the blip block.
I'm not exactly sure how to go about things, so any tips would be highly appreciated!

Looking forward to your reply!

Best Wishes,
Misho
Subject Author Posted

Adding a field map for rs-fMRI distortion correction

misho_dimitrov May 12, 2022 07:14AM

Re: Adding a field map for rs-fMRI distortion correction

rick reynolds May 12, 2022 10:30AM

Re: Adding a field map for rs-fMRI distortion correction

misho_dimitrov May 13, 2022 03:18AM

Re: Adding a field map for rs-fMRI distortion correction

misho_dimitrov June 07, 2022 02:19AM



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