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Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| May 19, 2023 03:19AM | |
Yes, the scan time is a little bit long. There are 1600 time points with TR=2s. Here is the full command and log. Could you please let me know how to modify it? Or can I split the full timeseries into two timeseries images with 800 time points each and merge them after finishing the preprocessing?
log:
Edited 1 time(s). Last edit at 05/19/2023 06:55AM by ptaylor.
afni_proc.py \
-subj_id ${subj} \
-blocks tshift align tlrc volreg blur mask scale regress \
-dsets ${dsets_epi} \
-copy_anat ${anat_cp} \
-anat_has_skull no \
-anat_uniform_method none \
-radial_correlate_blocks tcat volreg \
-radial_correlate_opts -sphere_rad 14 \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_warp_dxyz ${final_dxyz} \
-volreg_compute_tsnr yes \
-align_epi_strip_method 3dSkullStrip \
-tlrc_base ${ref_base} \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets ${dsets_NL_warp} \
-blur_size ${blur_size} \
-regress_motion_per_run \
-regress_apply_mot_types demean deriv \
-regress_censor_motion ${cen_motion} \
-regress_censor_outliers ${cen_outliers} \
-regress_est_blur_errts \
-regress_est_blur_epits \
-regress_run_clustsim no \
-html_review_style pythonic \
log:
++ Proc command: 20_ap_vox
++ Found 1 subj:
++ Prepare cmd for: sub-032163 --- ses-1
++ Executing 'swarm' cmd script: /Macaque/afni_test/swarm/swarm_20_ap_vox.tcsh
set subj = sub-032163
set ses = ses-1
set ap_label = 20_ap_vox
set dir_inroot = /Macaque/afni_test
set dir_log = /Macaque/afni_test/logs
set dir_ref = /Macaque/afni_test/NMT_v2.0_sym/NMT_v2.0_sym_05mm
set dir_basic = /Macaque/afni_test/BIDS
set dir_aw = /Macaque/afni_test/AFNI_aw
set dir_ap = /Macaque/afni_test/AFNI_ap
set sdir_basic = /Macaque/afni_test/BIDS/sub-032163/ses-1
set sdir_anat = /Macaque/afni_test/BIDS/sub-032163/ses-1/anat
set sdir_epi = /Macaque/afni_test/BIDS/sub-032163/ses-1/func
set sdir_aw = /Macaque/afni_test/AFNI_aw/sub-032163/ses-1
set sdir_ap = /Macaque/afni_test/AFNI_ap/sub-032163/ses-1
set anat_orig = /Macaque/afni_test/BIDS/sub-032163/ses-1/anat/sub-032163*T1w.nii.gz
set anat_orig_ab = sub-032163_anat
set ref_base = /Macaque/afni_test/NMT_v2.0_sym/NMT_v2.0_sym_05mm/NMT_v2.0_sym_05mm_SS.nii.gz
set ref_base_ab = NMT2
set ref_atl = ( /Macaque/afni_test/NMT_v2.0_sym/NMT_v2.0_sym_05mm/CHARM_in_NMT_v2.0_sym_05mm.nii.gz /Macaque/afni_test/NMT_v2.0_sym/NMT_v2.0_sym_05mm/D99_atlas_in_NMT_v2.0_sym_05mm.nii.gz )
set ref_atl_ab = ( CHARM D99 )
set ref_seg = /Macaque/afni_test/NMT_v2.0_sym/NMT_v2.0_sym_05mm/NMT_v2.0_sym_05mm_segmentation.nii.gz
set ref_seg_ab = SEG
set ref_mask = /Macaque/afni_test/NMT_v2.0_sym/NMT_v2.0_sym_05mm/NMT_v2.0_sym_05mm_brainmask.nii.gz
set ref_mask_ab = MASK
set dsets_epi = ( /Macaque/afni_test/BIDS/sub-032163/ses-1/func/sub-032163*bold.nii.gz )
set anat_cp = /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_nsu.nii.gz
set dsets_NL_warp = ( /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_warp2std_nsu.nii.gz /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_composite_linear_to_template.1D /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_shft_WARP.nii.gz )
set blur_size = 2.0
set final_dxyz = 1.25
set cen_motion = 0.1
set cen_outliers = 0.02
set cost_a2e = lpc+ZZ
set aea_extra =
set aea_uni_epi = yes
set nthr_avail = `afni_system_check.py -disp_num_cpu`
afni_system_check.py -disp_num_cpu
set nthr_using = `afni_check_omp`
afni_check_omp
echo ++ INFO: Using 12 of available 12 threads
++ INFO: Using 12 of available 12 threads
setenv AFNI_COMPRESSOR GZIP
set ap_cmd = /Macaque/afni_test/AFNI_ap/sub-032163/ses-1/ap.cmd.sub-032163
mkdir -p /Macaque/afni_test/AFNI_ap/sub-032163/ses-1
cat
cd /Macaque/afni_test/AFNI_ap/sub-032163/ses-1
tcsh -xef /Macaque/afni_test/AFNI_ap/sub-032163/ses-1/ap.cmd.sub-032163
tee output.ap.cmd.sub-032163
afni_proc.py -subj_id sub-032163 -blocks tshift align tlrc volreg blur mask scale regress -dsets /Macaque/afni_test/BIDS/sub-032163/ses-1/func/sub-032163_ses-001_task-resting_run-1_bold.nii.gz -copy_anat /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_nsu.nii.gz -anat_has_skull no -anat_uniform_method none -radial_correlate_blocks tcat volreg -radial_correlate_opts -sphere_rad 14 -volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp -volreg_warp_dxyz 1.25 -volreg_compute_tsnr yes -align_epi_strip_method 3dSkullStrip -tlrc_base /Macaque/afni_test/NMT_v2.0_sym/NMT_v2.0_sym_05mm/NMT_v2.0_sym_05mm_SS.nii.gz -tlrc_NL_warp -tlrc_NL_warped_dsets /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_warp2std_nsu.nii.gz /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_composite_linear_to_template.1D /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_shft_WARP.nii.gz -blur_size 2.0 -regress_motion_per_run -regress_apply_mot_types demean deriv -regress_censor_motion 0.1 -regress_censor_outliers 0.02 -regress_est_blur_errts -regress_est_blur_epits -regress_run_clustsim no -html_review_style pythonic
-- applying input view as +orig
-- template = 'NMT_v2.0_sym_05mm_SS.nii.gz', exists = 1
-- will use min outlier volume as motion base
-- including default: -find_var_line_blocks tcat
-- tcat: reps is now 1600
++ updating polort to 22, from run len 3212.0 s
-- importing NL-warp datasets
-- volreg: using base dset vr_base_min_outlier+orig
++ volreg: applying volreg/epi2anat/tlrc xforms to isotropic 1.25 mm tlrc voxels
-- masking: group anat = 'NMT_v2.0_sym_05mm_SS.nii.gz', exists = 1
-- have 1 ROI dict entries ...
-- will apply motion types: demean, deriv
-- using default: will not apply EPI Automask
(see 'MASKING NOTE' from the -help for details)
-------------------------------------
** warning have only 1 run to analyze
-------------------------------------
--> script is file: proc.sub-032163
to execute via tcsh:
tcsh -xef proc.sub-032163 |& tee output.proc.sub-032163
to execute via bash:
tcsh -xef proc.sub-032163 2>&1 | tee output.proc.sub-032163
tcsh -xef proc.sub-032163
tee output.proc.sub-032163
echo auto-generated by afni_proc.py, Fri May 19 15:01:51 2023
auto-generated by afni_proc.py, Fri May 19 15:01:51 2023
echo (version 7.55, March 1, 2023)
(version 7.55, March 1, 2023)
echo execution started: `date`
date
execution started: Fri May 19 15:01:52 CST 2023
afni -ver
Precompiled binary linux_ubuntu_16_64: May 8 2023 (Version AFNI_23.1.05 'Publius Helvius Pertinax')
afni_history -check_date 14 Nov 2022
-- is current: afni_history as new as: 14 Nov 2022
most recent entry is: 05 May 2023
if ( 0 ) then
if ( 0 > 0 ) then
set subj = sub-032163
endif
set output_dir = sub-032163.results
if ( -d sub-032163.results ) then
set runs = ( `count -digits 2 1 1` )
count -digits 2 1 1
mkdir -p sub-032163.results
mkdir sub-032163.results/stimuli
3dcopy /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_nsu.nii.gz sub-032163.results/sub-032163_anat_nsu
++ 3dcopy: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
3dcopy /Macaque/afni_test/NMT_v2.0_sym/NMT_v2.0_sym_05mm/NMT_v2.0_sym_05mm_SS.nii.gz sub-032163.results/NMT_v2.0_sym_05mm_SS.nii.gz
++ 3dcopy: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
3dcopy /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_warp2std_nsu.nii.gz sub-032163.results/sub-032163_anat_warp2std_nsu
++ 3dcopy: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
3dcopy /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_composite_linear_to_template.1D sub-032163.results/sub-032163_anat_composite_linear_to_template.1D
++ 3dcopy: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
3dcopy /Macaque/afni_test/AFNI_aw/sub-032163/ses-1/sub-032163_anat_shft_WARP.nii.gz sub-032163.results/sub-032163_anat_shft_WARP.nii.gz
++ 3dcopy: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
3dTcat -prefix sub-032163.results/pb00.sub-032163.r01.tcat /Macaque/afni_test/BIDS/sub-032163/ses-1/func/sub-032163_ses-001_task-resting_run-1_bold.nii.gz[0..$]
++ 3dTcat: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ elapsed time = 19.7 s
set tr_counts = ( 1600 )
cd sub-032163.results
@radial_correlate -nfirst 0 -polort 22 -do_clean yes -rdir radcor.pb00.tcat -sphere_rad 14 pb00.sub-032163.r01.tcat+orig.HEAD
++ 3dTcat: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ elapsed time = 23.0 s
++ 3dAutomask: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ Authored by: Emperor Zhark
-- detrend -polort 22, new eset = det.r01
++ 3dTproject: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
** FATAL ERROR: -polort value can't be over 20 
** Program compile date = May 8 2023
-- running correlation on dataset pb00.sub-032163.r01.tcat+orig.HEAD ...
++ merge blur: rad 14, FWHM 28
++ 3dmerge: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
*** cannot open dataset det.r01+orig
Program 3dmerge
3dmerge: edit and combine 3D datasets, by RW Cox
++ 3dTcorrelate: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
** FATAL ERROR: Can't open input dataset sphere.mean.14.r01+orig
** Program compile date = May 8 2023
++ 3dbucket: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
cp: No match.
---- done
++ have do_clean, cleaning up...
tee out.vlines.pb00.tcat.txt
find_variance_lines.tcsh -polort 22 -nerode 2 -rdir vlines.pb00.tcat pb00.sub-032163.r01.tcat+orig.HEAD
++ have nslices : 36
++ copying pb00.sub-032163.r01.tcat+orig.HEAD[0..$] to ts.0.orig.r01.nii.gz
++ 3dTcat: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ elapsed time = 52.3 s
++ creating automask from first dset
++ 3dAutomask: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset ts.0.orig.r01.nii.gz
++ Forming automask
+ Fixed clip level = 753.889526
+ Used gradual clip level = 573.789185 .. 992.627991
+ Number voxels above clip level = 18595
+ Clustering voxels ...
+ Largest cluster has 18333 voxels
+ Clustering voxels ...
+ Largest cluster has 17393 voxels
+ Filled 813 voxels in small holes; now have 18206 voxels
+ Filled 34 voxels in large holes; now have 18240 voxels
+ Clustering voxels ...
+ Largest cluster has 18236 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 129220 voxels
+ Mask now has 18236 voxels
++ 18236 voxels in the mask [out of 147456: 12.37%]
++ first 10 x-planes are zero [from R]
++ last 9 x-planes are zero [from L]
++ first 13 y-planes are zero [from P]
++ last 11 y-planes are zero [from A]
++ first 8 z-planes are zero [from I]
++ last 4 z-planes are zero [from S]
++ Output dataset ./mask.nii.gz
++ CPU time = 0.000000 sec
-- will apply mask mask.nii.gz
++ eroding mask.nii.gz by 2 voxels
++ no -frac option: defaulting to -union
++ processing 1 input dataset(s), NN=2...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 7176 survived, 140280 were zero
++ writing result mask.nii.gz...
++ Output dataset ./mask.nii.gz
++ requiring 5 voxels in mask columns
++ 3dLocalstat: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ Authored by: Emperor Zhark
++ Number of voxels in mask = 7176
++ Neighborhood comprises 73 voxels
++ Start sub-brick [0]
++ Output dataset ./tmp.mask.col.count.nii.gz
++ 3dcalc: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./mask.nii.gz
-- detrend -polort 22, new eset = ts.1.det.r01.nii.gz
++ 3dTproject: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
** FATAL ERROR: -polort value can't be over 20
** Program compile date = May 8 2023
++ 3dTstat: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ Authored by: KR Hammett & RW Cox
** FATAL ERROR: Can't open dataset ts.1.det.r01.nii.gz
** Program compile date = May 8 2023
++ 3dcalc: AFNI version=AFNI_23.1.05 (May 8 2023) [64-bit]
++ Authored by: A cast of thousands
** FATAL ERROR: can't open dataset tmp.stdev.nii.gz
** Program compile date = May 8 2023
rm: cannot remove 'tmp.stdev.nii.gz': No such file or directory
** FATAL ERROR: Can't open dataset 'var.0.orig.r01.nii.gz'
** Program compile date = May 8 2023
echo ++ FINISHED AP: 20_ap_vox
++ FINISHED AP: 20_ap_vox
exit 0
Edited 1 time(s). Last edit at 05/19/2023 06:55AM by ptaylor.
| Subject | Author | Posted |
|---|---|---|
|
Jewel | May 18, 2023 05:29AM |
|
ptaylor | May 18, 2023 09:41AM |
|
Jewel | May 19, 2023 03:19AM |
|
ptaylor | May 19, 2023 09:34AM |
|
rick reynolds | May 19, 2023 10:20AM |
|
Jewel | May 21, 2023 10:52PM |
