Hi AFNI Experts,
I have some fmriprep preprocessed data which I am looking to complete first and second level GLM task analysis in AFNI. I have followed a couple other threads on the subject (e.g. here and here). I am using AFNI version 23.2.04 and looking to run afni_proc.py blocks "blur mask scale regress".
In fmriprep, the following preprocessing steps have been completed: (1) head motion correction, (2) susceptibility distortion correction, (3) BOLD-T1w coregistration, (4) registration to MNI152 template, (5) confound estimation.
Before running the afni_proc.py script, I have successfully:
-
converted and concatenated fmriprep motion confounds from all runs to "dfile_rall.1D" (nframes x 6), ordered as roll, pitch, yaw (deg), dS, dL, dP (mm)
-
converted additional confounds of interest from fmriprep confounds.tsv to "confounds.txt" where run confounds are zero padded so each run's confound has 1 column, and stacked across runs. For example: run01_global_signal, run02_global_signal (nfames x nconfounds)
**where nframes are the number of time points across all runs (1258 + 1258) -
stored events timing as .1D files with local timing vectors
I am using the afni_proc.py command:
[truncated]
++ have do_clean, cleaning up...
gen_epi_review.py -script @epi_review.101 -dsets pb00.101.r01.tcat+tlrc.HEAD pb00.101.r02.tcat+tlrc.HEAD
cat
cat out.ap_uvars.txt
afni_python_wrapper.py -eval data_file_to_json()
gen_ss_review_scripts.py -exit0 -init_uvars_json out.ap_uvars.json -write_uvars_json out.ss_review_uvars.json
** failed to find volreg dset, continuing...
** failed to guess final_anat (continuing)
** failed to guess align_anat (continuing)
** failed to guess volreg base dset (continuing)
** failed to guess align_anat (continuing)
++ writing ss review basic: @ss_review_basic
** no final_anat, skipping align check...
** no volreg_dset, skipping align check...
++ writing ss review driver: @ss_review_driver
++ writing ss review drive commands: @ss_review_driver_commands
rm -f rm.errts.unit+tlrc.BRIK rm.errts.unit+tlrc.HEAD rm.mask_r01+tlrc.BRIK.gz rm.mask_r01+tlrc.HEAD rm.mask_r02+tlrc.BRIK.gz rm.mask_r02+tlrc.HEAD rm.mean_r01+tlrc.BRIK rm.mean_r01+tlrc.HEAD rm.mean_r02+tlrc.BRIK rm.mean_r02+tlrc.HEAD rm.noise.all+tlrc.BRIK rm.noise.all+tlrc.HEAD rm.out.cen.r01.1D rm.out.cen.r02.1D rm.signal.all+tlrc.BRIK rm.signal.all+tlrc.HEAD
if ( -e @ss_review_basic ) then
./@ss_review_basic
tee out.ss_review.101.txt
subject ID : 101
AFNI version : AFNI_23.2.04
AFNI package : linux_ubuntu_16_64
TR : 0.46
TRs removed (per run) : 22
multiband level : 1
slice timing pattern : simult
num stim classes provided : 3
final stats dset : stats.101_REML+tlrc.HEAD
orig voxel counts : 61 73 61
orig voxel resolution : 3.024000 3.024000 3.000000
orig volume center : -0.720001 17.136002 18.000000
final voxel resolution : 3.024000 3.024000 3.000000
motion limit : 0.3
num TRs above mot limit : 7
average motion (per TR) : 0.084016
average censored motion : 0.0826319
max motion displacement : 3.87307
max censored displacement : 2.69611
outlier limit : 0.1
average outlier frac (TR) : 0.00107248
num TRs above out limit : 1
num runs found : 2
num TRs per run : 1258 1258
num TRs per run (applied) : 1258 1249
num TRs per run (censored): 0 9
fraction censored per run : 0 0.00715421
TRs total (uncensored) : 2516
TRs total : 2507
degrees of freedom used : 27
degrees of freedom left : 2480
final DF fraction : 0.985692
TRs censored : 9
censor fraction : 0.003577
num regs of interest : 3
num TRs per stim (orig) : 72 265 217
num TRs censored per stim : 0 0 0
fraction TRs censored : 0.000 0.000 0.000
ave mot per sresp (orig) : 0.078362 0.081972 0.077312
ave mot per sresp (cens) : 0.078362 0.081972 0.077312
TSNR average : 197.925
global correlation (GCOR) : 0.0732032
maximum F-stat (masked) : 66.8671
blur estimates (ACF) : 0.735122 4.22917 13.3962
blur estimates (FWHM) : 0 0 0
apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
+* WARN: no main dset (not template, anat_final nor vr_base)
++ Done making (executable) IC errts script:
run_instacorr_errts.tcsh
++ Done making (executable) GV errts script:
run_graphview_errts.tcsh
++ Done making (executable) IC pbrun script:
run_instacorr_pbrun.tcsh
++ Done making (executable) GV pbrun script:
run_graphview_pbrun.tcsh
++ APQC create: qc_00_vorig_anat
Traceback (most recent call last):
File "/root/abin//apqc_make_tcsh.py", line 471, in <module>
cmd = lat.apqc_vorig_all( ap_ssdict, obase, "vorig", "anat",
File "/root/abin/afnipy/lib_apqc_tcsh.py", line 2171, in apqc_vorig_all
with open(pbar_json, 'r') as fff:
FileNotFoundError: [Errno 2] No such file or directory: 'QC_101/media/qc_00_vorig_anat.pbar.json'
Thanks in advance for any advice.
Amy