Good afternoon,

I have two questions regarding the quality control report that is generated after running afni_proc.py, which I am using to preprocess my resting state fMRI data set. Please see below for my afni_proc.py

	afni_proc.py -subj_id ${subj} \
	-script proc.${subj} -scr_overwrite \
	-blocks despike tshift align tlrc volreg blur mask regress \
	-out_dir $outputDir \
	-copy_anat $sdir/${anatsubj}_SurfVol+orig \
	-anat_follower_ROI aaseg anat $sdir/aparc.a2009s+aseg.nii \
	-anat_follower_ROI aeseg epi  $sdir/aparc.a2009s+aseg.nii \
	-anat_follower_ROI FSVente epi $sdir/${anatsubj}_vent.nii \
	-anat_follower_ROI FSWe epi $sdir/${anatsubj}_WM.nii \
	-anat_follower_erode FSVente FSWe \
	-dsets $dataIn \
	-tshift_opts_ts -tpattern seq+z -TR 2s \
	-align_opts_aea -cost lpc+ZZ -ginormous_move \
	-tlrc_base MNI152_T1_2009c+tlrc \
	-tlrc_NL_warp \
	-volreg_align_to MIN_OUTLIER \
	-volreg_align_e2a \
	-volreg_tlrc_warp \
	-mask_segment_anat yes \
	-mask_segment_erode yes \
	-blur_size 6.0 \
	-regress_motion_per_run \
	-regress_ROI_PC FSVente 3 \
	-regress_make_corr_vols aeseg FSVente \
	-regress_anaticor_fast \
	-regress_anaticor_label FSWe \
	-regress_censor_motion 0.4 \
	-regress_censor_outliers 0.1 \
	-regress_bandpass 0.01 0.1 \
	-regress_apply_mot_types demean deriv \
	-regress_est_blur_epits \
	-regress_est_blur_errts \

Question #1: When I look at the QC report generated (QC/index.html), all looks good, except the 'qc_10_regr_grayplot.jpg' file is an empty file. However, if I run the @ss_review_driver, I can see the enorm, outlier, and censoring information without an issue. Would you let me know what may be going on?

Question #2: When I run the @ss_review_driver, I get the following error messages.

** ERROR: mri_read_ascii: can't read any valid data from file X.stim.xmat.1D
** FATAL ERROR: Can't read input file 'X.stim.xmat.1D' iarg=2

and

------------- 3dDeconvolve.err -------------
*+ WARNING: !! in Signal+Baseline matrix:
 * Largest singular value=2.51615
 * 4 singular values are less than cutoff=2.51615e-07
 * Implies strong collinearity in the matrix columns! 
*+ WARNING: !! in Baseline-only matrix:
 * Largest singular value=2.51615
 * 4 singular values are less than cutoff=2.51615e-07
 * Implies strong collinearity in the matrix columns! 
--------------------------------------------

Am I getting these messages because this is a resting state data, or there is something else (perhaps related to my Question #1?) going on?

Question #3: This has nothing to do with the last 2 questions, but I was wondering. Would you mind explaining what would adding the following code to my afni_proc.py script would do? I have read the help file multiple times, but I'm still having trouble understanding what the code is doing.

-tlrc_NL_warped_dsets anatQQ.FT.nii anatQQ.FT.aff12.1D  anatQQ.FT_WARP.nii

Thank you in advance for your help,
Ann



Edited 1 time(s). Last edit at 03/02/2021 10:04PM by annschoe.