AFNI version info (afni -ver): AFNI_23.1.10
Hello,
I have been testing the code from MACAQUE_DEMO from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9272767/#S18
The scripts run fine and as expected, but when looking at the QC (quality control) folders for afni_proc.py on all EPI runs and comparing it with Figure 10 of the paper or the ''QC_sub-000-ALLEPI'', the results do not match. It doesn't show any thresholding/colour spot and it fails to include the final gltsym, ''+.5FO''.
My output vs. expected output:
Any help is greatly appreciated.
The following are part my own generated out.review_html and @ss_review_html respectively (the demo does not provide these files related to the processing, only the QC folders:
++ My command:
@chauffeur_afni -ulay ./NMT_v2.1_sym_05mm_SS.nii.gz -box_focus_slices ./NMT_v2.1_sym_05mm_SS.nii.gz -olay stats.sub-000+tlrc.HEAD -cbar Reds_and_Blues_Inv -pass -ulay_range 0% 120% -func_range 0.000000 -thr_olay 99.99 -olay_alpha Yes -olay_boxed Yes -set_subbricks 0 13 14 -opacity 9 -pbar_saveim QC_sub-000/media/qc_07_vstat_+F-SF_GLT_0_Coef.pbar.jpg -pbar_comm_range 99%ile in suprathresh mask voxels -pbar_comm_thr two-sided p=0.001, alpha+boxed on -prefix QC_sub-000/media/qc_07_vstat_+F-SF_GLT_0_Coef -save_ftype JPEG -montx 7 -monty 1 -montgap 1 -montcolor black -set_xhairs OFF -label_mode 1 -label_size 4 -no_cor -do_clean
++ Using AFNI ver : AFNI_23.1.10
++ chauffeur ver : 6.52
------------------ start of optionizing ------------------
++ Found input file: ./NMT_v2.1_sym_05mm_SS.nii.gz
++ Found input file: stats.sub-000+tlrc.HEAD
++ Found focus refbox file: ./NMT_v2.1_sym_05mm_SS.nii.gz
++ Using blowup factor: 2
++ Using opacity: 9
++ Making temporary work directory to copy vis files: QC_sub-000/media/__tmp_chauf_iJ5aBhpffSt
++ Converted 0 to labels
++ Final subbrick indices: 0 13 14
bc: Command not found.
++ Copy ulay to visualize (volumetric) within user's range:
bc: Command not found.
bc: Command not found.
bc: Command not found.
++ Ulay to be visualized within user range:
[0%, 120%] -> [0.000000, ]
++ 3dcalc: AFNI version=AFNI_23.1.10 (Jun 30 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-000/media/__tmp_chauf_iJ5aBhpffSt/tmp_ulay.nii
++ 3dcalc: AFNI version=AFNI_23.1.10 (Jun 30 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./QC_sub-000/media/__tmp_chauf_iJ5aBhpffSt/tmp_olay.nii
++ User-entered function range value value (0.000000)
++ Dimensions (xyzt): 128 156 100 1
++ (initial) Slice spacing ordered (x,y,z) is: 18 22 14
++ 3dAutobox: AFNI version=AFNI_23.1.10 (Jun 30 2023) [64-bit]
++ Auto bbox: x=5..122 y=3..148 z=0..95
++ 3dAutobox: output dataset = QC_sub-000/media/__tmp_chauf_iJ5aBhpffSt/ulay_box_0.nii
bc: Command not found.
bc: Command not found.
bc: Command not found.
bc: Command not found.
@: Expression Syntax.
++ How many coors? 0
++ Will have the ref box central coors : SET_DICOM_XYZ
++ Will have the ref box central gapord: 16 20 13
------------------- end of optionizing -------------------
# ================= view stats (+ eff est): +F-SF_GLT_0_Coef =================
# peruse statistical results:
# thr vol [14]
# olay vol [13] for pbar
set opref = qc_07_vstat_+F-SF_GLT_0_Coef
set ulay_dset = ${main_dset}
set focus_box = ${main_dset}
set ulay_name = `3dinfo -prefix ${ulay_dset}`
set olay_name = `3dinfo -prefix ${stats_dset}`
set avsp = `3dinfo -av_space ${stats_dset}`
set olaybrick = 13
set olaylabel = `3dinfo -label ${stats_dset}"[${olaybrick}]"`
set thrbrick = 14
set thrlabel = `3dinfo -label ${stats_dset}"[${thrbrick}]"`
set thr_staux = `3dAttribute BRICK_STATAUX ${stats_dset}"[${thrbrick}]"`
set thr_dof = `echo ${thr_staux[4-]}`
set tjson = _tmp.txt
set ojson = ${odir_img}/${opref}.axi.json
set tjson2 = _tmp2.txt
set ojson2 = ${odir_img}/${opref}.sag.json
set opbarrt = ${odir_img}/${opref}.pbar
set tcoef = __tmp_coef_vol.nii
set thr_thresh = `p2dsetstat \
-quiet \
-inset ${stats_dset}"[${thrlabel}]" \
-2sided \
-pval 0.001`
3dcalc \
-a "${stats_dset}[${olaylabel}]" \
-b "${stats_dset}[${thrlabel}]" \
-c ${mask_dset} \
-expr "abs(a)*step(b-${thr_thresh})*step(c)" \
-prefix ${tcoef}
set ppcoef = `3dBrickStat \
-slow \
-non-zero \
-percentile 99 1 99 \
${tcoef}`
set olay_topval = ${ppcoef[2]}
set olay_botval = -${olay_topval}
@chauffeur_afni \
-ulay ${ulay_dset} \
-box_focus_slices ${focus_box} \
-olay ${stats_dset} \
-cbar Reds_and_Blues_Inv \
-pass \
-ulay_range 0% 120% \
-func_range ${olay_topval} \
-thr_olay ${thr_thresh} \
-olay_alpha Yes \
-olay_boxed Yes \
-set_subbricks 0 ${olaybrick} ${thrbrick} \
-opacity 9 \
-pbar_saveim "${opbarrt}.jpg" \
-pbar_comm_range "99%ile in suprathresh mask voxels" \
-pbar_comm_thr "two-sided p=0.001, alpha+boxed on" \
-prefix "${odir_img}/${opref}" \
-save_ftype JPEG \
-montx 7 -monty 1 \
-montgap 1 \
-montcolor 'black' \
-set_xhairs OFF \
-label_mode 1 -label_size 4 \
-no_cor \
-do_clean
\rm ${tcoef}*
The code is from the ''do_21_ap_all.tcsh'' script, unchanged from when MACAQUE_DEMO is installed.
-regress_stim_labels ${stim_labs} \
-regress_opts_3dD \ \
-gltsym 'SYM: +FACE -SFACE' -glt_label 1 +F-SF \
-gltsym 'SYM: +OBJ -SOBJ' -glt_label 2 +O-SO \
-gltsym 'SYM: +FACE -SFACE +OBJ -SOBJ' -glt_label 3 +INTACT-SCRAM \
-gltsym 'SYM: +FACE -OBJ' -glt_label 4 +F-O \
-gltsym 'SYM: +.5*FACE +.5*OBJ' -glt_label 5 +.5FO \
-regress_basis 'MIONN(36)'
