Hi Paul,
here is the output of
@djunct_overlap_check \
-ulay DSET_ANATOMICAL \
-olay DSET_EPI \
-prefix img_epi_anat_olap
for the same subject that I showed before. Please see the first attached image. I am not sure if that overlap is good enough. The problem is that AFNI proc alignment fails (note that the SSwarper results are really clean and nice, so the problem is not comming from badly processed skullstripping).
Another problem is the following message while preprocessing the subject with AFNI proc:
*+ WARNING: Input dataset is not 3D+time; assuming TR=1.0
I know that this is a “standard” output by AFNI proc that can normally be ignored. And in previous datasets that I preprocessed, the final TR that is stated at the end of the index page (I am talking about the quality control output file by AFNI proc) showed the real TR of the dataset, for example TR = 1, or TR = 2.0, etc. But with this dataset, the index QC page shows me a TR of 1 after preprocessing, even though the real TR of that dataset is 2.27.
I then checked the TR via 3dinfo of the functional raw data, and the functional raw data inded has a TR of 1, even though that is wrong. Would it be fine shifting the TR to 2.27 via 3drefit in the previously shown code that I also use to deoblique the functional runs?
Yet another potential problem I have never seen before is the following output in the index file:
EPI variance lines warnings
Lines per run : 1
Coordinates (check locations with InstaCorr)
--------------------------------------------
r01
-----------------------
-57.70 12.80 6.40
Can this be ignored, or is that relevant?
Here is my AFNI proc script. This is a resting-state run. I previously ran it with “lpc+ZZ” (instead of lpa) and without “-align_unifize_epi local”, but the results looked messed up in both cases. I attached you screenshots for both results.
afni_proc.py \
-subj_id ${subject}_EoEc \
-out_dir $directory_run/Results \
-dsets \
$directory_deoblique/Eo-Ec_deoblique+orig \
-blocks despike tshift align tlrc volreg mask blur regress \
-copy_anat $directory_sswarper/anatSS.$subject.nii \
-anat_has_skull no \
-tcat_remove_first_trs 4 \
-align_opts_aea -cost lpa -big_move \
-align_unifize_epi local \
-volreg_align_e2a \
-volreg_align_to MIN_OUTLIER \
-volreg_tlrc_warp -tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
$directory_sswarper/anatQQ.$subject.nii \
$directory_sswarper/anatQQ.$subject.aff12.1D \
$directory_sswarper/anatQQ.${subject}_WARP.nii \
-volreg_post_vr_allin yes \
-volreg_pvra_base_index MIN_OUTLIER \
-mask_segment_anat yes \
-mask_segment_erode yes \
-regress_anaticor \
-regress_ROI WMe CSFe \
-regress_apply_mot_types demean deriv \
-regress_motion_per_run \
-regress_censor_motion 0.3 \
-regress_censor_outliers 0.15 \
-blur_size 8.0 \
-regress_est_blur_epits \
-regress_est_blur_errts \
-html_review_style pythonic \
-execute
Thanks for any help.
Update:
I used 3drefit to change the TR from 1.0 to 2.27 before running deoblique on the functional raw data. The EPI variance lines warning no longer appears after preprocessing the first subject with AFNI proc. However, alignment still fails. I already tried out the lpa, lpc+zz, and nmi cost functions.
Update two:
Simply running the following alignment options
-align_opts_aea -cost lpc+zz -giang_move \
-align_unifize_epi local \
did the job. Hence, -giant_move instead of only running -big_move was required here. Sometimes the solutions are easier than I thought…