AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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January 05, 2021 01:10PM
I apologize for being rather vague! This would be for a task-based analysis. fmriprep yields preprocessed files along with a .tsv file of nuisance regressors. Ideally, I would like to implement something like Example 6b, but starting after blur:

afni_proc.py \
-subj_id FT.e6b \
-copy_anat Qwarp/anat_warped/anatSS.FT.nii \
-anat_has_skull no \
-anat_follower anat_w_skull anat FT/FT_anat+orig \
-dsets FT/FT_epi_r?+orig.HEAD \
-blocks tshift align tlrc volreg blur mask scale regress \
-radial_correlate_blocks tcat volreg \
-tcat_remove_first_trs 2 \
-align_opts_aea -cost lpc+ZZ -giant_move -check_flip \
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets Qwarp/anat_warped/anatQQ.FT.nii \
Qwarp/anat_warped/anatQQ.FT.aff12.1D \
Qwarp/anat_warped/anatQQ.FT_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-mask_epi_anat yes \
-blur_size 4.0 \
-regress_stim_times FT/AV1_vis.txt FT/AV2_aud.txt \
-regress_stim_labels vis aud \
-regress_basis 'BLOCK(20,1)' \
-regress_opts_3dD -jobs 2 -gltsym 'SYM: vis -aud' \
-glt_label 1 V-A \
-regress_motion_per_run \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.05 \
-regress_3dD_stop \
-regress_reml_exec \
-regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no \
-html_review_style pythonic \
-execute

I have already implemented post-fmriprep first-level analysis using 3DDeconvolve (somewhat) through nipype, using the ortvec option to adjust for a subset of regressors from the .tsv file. But I think that it may be better to use afni_proc.py if I am using AFNI, for a number of reasons. I guess my more precise question is: Is there a way to directly imput the preprocessed file and "ortvec" option into the -regress line of afni_proc.py task-based analysis? Thank you!!
Subject Author Posted

fmriprep to afni_proc.py?

dani2 January 04, 2021 02:13PM

Re: fmriprep to afni_proc.py?

ptaylor January 05, 2021 09:19AM

Re: fmriprep to afni_proc.py?

dani2 January 05, 2021 01:10PM

Re: fmriprep to afni_proc.py?

Peter Molfese January 05, 2021 09:56PM

Re: fmriprep to afni_proc.py?

dani2 January 14, 2021 10:32AM

Re: fmriprep to afni_proc.py?

ptaylor January 14, 2021 11:51AM

Re: fmriprep to afni_proc.py?

MXD2019 June 16, 2021 02:20PM

Re: fmriprep to afni_proc.py?

ptaylor June 16, 2021 04:05PM