AFNI version info (afni -ver): AFNI_23.2.11
Hi there! I'm receiving some issues when trying to run afni_proc.py. The first issue is, when I run afni_proc.py, it thinks that there is only 1 run to analyze in the anat and func images I provided, but there are actually two runs. Unfortunately, the scanner was never stopped in between runs. Second, I keep receiving the warning message that -cmass is turned off, however, I thought align_opts_aea turned cmass on? Lastly, I am receiving this error in my output, that stops afni_proc.py from fully running:
3dAllineate -base anatSS.ATN001v1_ON_ns+orig -input rm.epi.all1+tlrc -1Dmatrix_apply mat.r01.warp.aff12.1D -mast_dxyz 2 -final NN -quiet -prefix rm.epi.1.r01
++ 3dAllineate: AFNI version=AFNI_23.2.11 (Sep 26 2023) [64-bit]
++ Authored by: Zhark the Registrator
e[7m*+ WARNING:e[0m If you are performing spatial transformations on an oblique dset,
such as ./rm.epi.all1+tlrc.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./rm.epi.all1+tlrc.BRIK is 19.635971 degrees from plumb.
++ NOTE: base and source coordinate systems have different handedness
+ Orientations: base=Right handed (LPI); source=Left handed (RPI)
+ - It is nothing to worry about: 3dAllineate aligns based on coordinates.
+ - But it is always important to check the alignment visually to be sure.
e[7m*+ WARNING:e[0m center of mass shifts (-cmass) are turned off, but would be large
e[7m*+ WARNING:e[0m - at least one is more than 20% of search range
+ -cmass x y z shifts = -1.111 -38.363 -22.990
+ shift search range is +/- = 57.459 81.855 81.855
+ 1.9% 46.9% 28.1%
++ 3dAllineate: total CPU time = 497.2 sec Elapsed = 123.6
+
++ ***********************************************************
e[7m*+ WARNING:e[0m -cmass was turned off, but might have been needed :(
+ Please check your results - PLEASE PLEASE PLEASE
++ ***********************************************************
3dTstat -min -prefix rm.epi.min.r01 rm.epi.1.r01+tlrc
++ 3dTstat: AFNI version=AFNI_23.2.11 (Sep 26 2023) [64-bit]
++ Authored by: KR Hammett & RW Cox
e[7m** FATAL ERROR:e[0m Can't open dataset rm.epi.1.r01+tlrc
** Program compile date = Sep 26 2023
Here is my afni_proc.py script
#!/bin/tcsh
afni_proc.py \
-subj_id ATN001v1_ON \
-copy_anat ./AFNI_SS_opt/ATN001v1_ON/anatSS.ATN001v1_ON.nii \
-anat_has_skull no \
-anat_follower anat_w_skull anat ./fMRIdata_DICOMsort/ATN001v1_ON/Nifti/"ATN001v1_ON_T1-MPRAGE-8min_20211223085844_301.nii.gz" \
-dsets ./fMRIdata_DICOMsort/ATN001v1_ON/Nifti/"ATN001v1_ON_MB3_fMRI-12min_Series0601.nii" \
-blocks tshift align tlrc volreg mask blur \
scale regress \
-radial_correlate_blocks tcat volreg \
-tcat_remove_first_trs 2 \
-align_unifize_epi local \
-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 ./AFNI_SS_opt/ATN001v1_ON/anatQQ.ATN001v1_ON.nii \
./AFNI_SS_opt/ATN001v1_ON/anatQQ.ATN001v1_ON.aff12.1D \
./AFNI_SS_opt/ATN001v1_ON/anatQQ.ATN001v1_ON_WARP.nii \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_compute_tsnr yes \
-mask_epi_anat yes \
-blur_size 3.0 \
-regress_stim_times ./VDR_data/events/ATN_001v1_ON_events.txt \
-regress_stim_types AM2 \
-regress_basis 'BLOCK(3,1)' \
-regress_opts_3dD -jobs 8 \
-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