AFNI proc creates empty qc_12_mot_grayplot.jpg (0 bytes) after preprocessing

AFNI Message Board
1

AFNI version info (AFNI_26.1.04 'Balbinus'; Mac M1 26.5.1 (25F80)):

I just preprocessed two runs of one subject via AFNI proc (after a long time not using AFNI proc and after recently updating AFNI). Everything is good except that, while in both runs AFNI proc creates the file qc_12_mot_grayplot.jpg, the file actually remains empty with zero bytes, hence it of course doesn’t show up in the QC index html.

afni_system_check.py -check_all

yields no errors and everything is installed properly. I have matplotlib etc. installed.

Also, the output.proc didn't seem to complain concerning the grayplot "++ APQC create: qc_12_mot_grayplot" with no error message as far as I can see. What might be interesting is that in the media folder of QC, qc_21_warns_press.dat and qc_22_warns_sat_4095.dat are also zero byte files.

Is this a simple and common bug easy to fix, or probably something more complicated? Any ideas where to start looking to fix this?

Thanks,

Philipp

2

Hi, Philipp-

The grayplot thing will happen sometimes when dependencies are not all installed.

Can you please go into your AP results directory and run:

apqc_make_tcsh.py -do_log -run

... and send me the log_apqc_tcsh.txt that that should create? It logs the stdout and stderr of programs run during the APQC HTML-generating process.

And could you please send me the system check (like, the ASC.txt file created by running):

afni_system_check.py -check_all > ASC.txt

?

thanks,
pt

3

Hi,

I send you both the log_apqc_tcsh.txt and the ASC.txt.

Philipp

4

Hi, Philipp-

Great, thanks.

And just to be sure, what was your AP command that was run, which produced this error?

thanks,
pt

5

The following was my AP code:

runs=(Rest Movie)

dir_sswarper=/volumes/sandisk1/sam_dataset/Processed/sswarper/Sam

for run in $runs; do

	mkdir -p /volumes/sandisk1/Sam_dataset/Processed/Preprocessing_${run}/Sam
	dir_func=/volumes/sandisk1/sam_dataset/raw/sam/functional_${run}
	dir_out=/volumes/sandisk1/sam_dataset/Processed/Preprocessing_${run}/sam

	cd $dir_out

	afni_proc.py \
	-subj_id Sam_${run} \
	-out_dir $dir_out/Results \
	-dsets $dir_func/${run}_Sam+orig \
	-blocks despike tshift align tlrc volreg mask scale regress \
	-copy_anat $dir_sswarper/anatSS.Sam.nii \
	-anat_has_skull no \
	-align_unifize_epi local \
	-align_opts_aea -cost lpc+ZZ \
					-giant_move \
					-check_flip \
	-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 \
		$dir_sswarper/anatQQ.Sam.nii \
		$dir_sswarper/anatQQ.Sam.aff12.1D \
		$dir_sswarper/anatQQ.Sam_WARP.nii \
	-volreg_post_vr_allin yes \
	-volreg_pvra_base_index MIN_OUTLIER \
	-mask_segment_anat yes \
	-mask_segment_erode yes \
	-regress_polort 2 \
	-regress_anaticor \
	-regress_ROI CSFe \
	-regress_apply_mot_types demean deriv \
	-regress_motion_per_run \
	-regress_censor_motion 0.4 \
	-regress_skip_first_outliers 5 \
	-html_review_style pythonic \
	-execute
done