afni.nimh.nih.gov

Hi AFNI gurus,

I am adapting another user's afni preprocessing script for my data and have run into some errors. Would you be able to take a look and let me know what might be wrong?

I listed some of the main errors is below. The IT department installed the Netpbm software for me, so I am unsure about why this issue is still coming up. I use: module load tools/netpbm-10.73.32

** ERROR: Xvfb -- not found in path -- @snapshot_volreg fails
** WARNING: this script cannot run without installing package netpbm11
** ERROR: Xvfb -- not found in path -- @snapshot_volreg fails
** WARNING: this script cannot run without installing package netpbm11
** warning: removing first 2 TRs from beginning of each run
--> the stimulus timing files must reflect the removal of these TRs
** WARNING: anat follower does not seem to exist: /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/s2000.nii
originally from /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/s2000.nii
** -tlrc_anat dataset '/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/anatSS.s2000.nii' does not exist
** invalid block : tlrc
----------------------------------------------------------------------
** failed command (create_blocks):

Another issue is these errors. I am confused because when I go to the location of my output directory, it says there are no files. Is there another way to clear intermediate outputs when I'm rerunning the script?
** ERROR: output dataset name 'anatSS.s2000.nii' conflicts with existing file
** ERROR: dataset NOT written to disk!

** ERROR: output dataset name 'anatQQ.s2000.nii' conflicts with existing file
** ERROR: dataset NOT written to disk!
** ERROR: output dataset name 'anatQQ.s2000_WARP.nii' conflicts with existing file
** ERROR: dataset NOT written to disk!

Thank you! I am not an experienced afni user so I apologize if these are silly questions! I have attached both my script and the full output below.

Best,
Leah

---
Here is my script:
#! /bin/tcsh

set subjID = s2000
set out_dir = /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data
set anat_dir = /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/anat

@SSwarper \
-input $anat_dir/anat+orig \
-base MNI152_2009_template_SSW.nii.gz \
-subid s2000 \
-odir ${out_dir}/anat.SSwarper \

#Then execute the preprocessing:

######################################################
# SPECIFY PARAMETERS FOR AFNI_PROC.PY
######################################################

#!/bin/tcsh

set subjID = s2000
set outdir = /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results
set stimdir = /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/stimuli
set epidir = /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/epi
set anatdir = /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/anat
set dsets = /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/

afni_proc.py -subj_id s2000 \
-script proc.script.s2000 \
-out_dir $outdir \
-scr_overwrite \
-blocks despike tshift align tlrc volreg mask blur scale regress \
-radial_correlate_blocks tcat volreg \
-copy_anat $outdir/anat.SSwarper/anatSS.s2000.nii \
-anat_follower anat_w_skull anat $outdir/anat.SSwarper/s2000.nii \
-tcat_remove_first_trs 2 \
-dsets \
$epidir/epi_r01+orig \
$epidir/epi_r02+orig \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-align_opts_aea -check_flip -cost lpc+zz -giant_move -AddEdge \
-blur_size 6 \
-blur_to_fwhm \
-anat_has_skull no \
-volreg_tlrc_warp \
-tlrc_base MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
$outdir/anat.SSwarper/anatQQ.s2000.nii \
$outdir/anat.SSwarper/anatQQ.s2000.aff12.1D \
$outdir/anat.SSwarper/anatQQ.s2000_WARP.nii \
-mask_epi_anat yes \
-regress_stim_times $stimdir/s2000__realcry_timing.1D \
$stimdir/s2000__controlcry_timing.1D \
$stimdir/s2000_realcrynoise_timing.1D \
$stimdir/s2000_controlnoise_timing.1D \
-regress_stim_labels \
realcry controlcry realcrynoise controlnoise \
-regress_basis 'BLOCK(20,1)' \
-regress_local_times \
-regress_motion_per_run \
-regress_censor_motion 0.5 \
-regress_censor_outliers 0.1 \
-regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_reml_exec
-regress_compute_fitts \
-regress_opts_3dD \
-bout \
-jobs 12 \
-num_glt 1 \
-gltsym 'SYM: +realcry +controlcry +realcrynoise +controlnoise' -glt_label 1 PosControl \
-execute \

--

Here are the errors:

[lgrande2@du-hpc ~]$ ssh -X node2
Last login: Wed Mar 25 11:58:38 2020 from hpc-io
[lgrande2@node2 ~]$ module load apps/afni-19.2.04
[lgrande2@node2 ~]$ module load apps/R-3.3.3
[lgrande2@node2 ~]$ module load tools/netpbm-10.73.32
[lgrande2@node2 ~]$ cd /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/scripts/AFNI_scripts
[lgrande2@node2 AFNI_scripts]$ tcsh afni_proc_Leah_remove_opts_reml
++ Starting: @SSwarper v1.52
++ Default OMP_NUM_THREADS is 8
++ OpenMP thread count = 8

+++ Command Echo:
3dQwarp -lite -base /usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz[1] -source /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUA.s2000.nii -weight /usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz[2] -allineate -noneg -maxlev 5 -iwarp -awarp -workhard:3:5 -prefix /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5.nii

++ 3dQwarp: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUA.s2000.nii,
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:/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUA.s2000.nii is 2.861839 degrees from plumb.
++ ###############################################################
+ Starting 3dAllineate (affine register) command:

3dAllineate -base /usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz[1] -source /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUA.s2000.nii -prefix XYZ_DkqH2ByQTRLbeghBR8mZ1g.nii -1Dmatrix_save XYZ_DkqH2ByQTRLbeghBR8mZ1g -cmass -final wsinc5 -float -master BASE -twobest 7 -weight /usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz[2] -zclip -fineblur 4.44
+ ###############################################################
++ 3dAllineate: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUA.s2000.nii,
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:/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUA.s2000.nii is 2.861839 degrees from plumb.
++ Source dataset: /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUA.s2000.nii
++ Base dataset: /usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz
++ Loading datasets
++ 3738596 voxels in source_automask+0
++ Zero-pad: xbot=22 xtop=21
++ Zero-pad: ybot=16 ytop=25
++ Zero-pad: zbot=22 ztop=16
++ 3510862 voxels [23.9%] in weight mask
++ Number of points for matching = 1650105
++ NOTE: base and source coordinate systems have different handedness
+ Orientations: base=Right handed (LPI); source=Left handed (ASR)
+ - It is nothing to worry about: 3dAllineate aligns based on coordinates.
+ - But it is always important to check the alignment visually to be sure.
++ OpenMP thread count = 8
++ ======= Allineation of 1 sub-bricks using Hellinger metric =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***
+ Final fine fit Parameters:
x-shift= -7.9514 y-shift=-17.8777 z-shift= 0.7282 ... enorm= 19.5798 mm
z-angle= -0.8219 x-angle= 17.2285 y-angle= 1.1239 ... total= 17.2762 deg
x-scale= 0.9563 y-scale= 0.8780 z-scale= 0.8441 ... vol3D= 0.7088 = base bigger than source
y/x-shear= -0.0012 z/x-shear= -0.0117 z/y-shear= -0.0557
++ Output dataset ./XYZ_DkqH2ByQTRLbeghBR8mZ1g.nii
++ Wrote -1Dmatrix_save XYZ_DkqH2ByQTRLbeghBR8mZ1g.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 403.9
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################

++ 3dQwarp: replacing source dataset with 3dAllineate result /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5_Allin.nii
+ 3dAllineate output files have been renamed
# mat44 3dAllineate matrix:
0.956130 -0.008160 -0.017916 -7.951410
0.010926 0.838528 0.260069 -17.877701
0.001088 -0.296821 0.791815 0.728203
++ Dataset zero-pad: xbot=21 xtop=20 ybot=15 ytop=24 zbot=21 ztop=15 voxels
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5_Allin.nii
++ AFNI warpomatic: 234 x 268 x 229 volume ; autobbox = 27..206 28..240 27..201 [clock= 6m 49s 172ms]
lev=0 5..228 2..266 6..222: [first cost=-0.57872] ..... done [cost:-0.57872==>-0.65470]
lev=1 patch=167x199x163 [clock= 10m 48s 672ms]........ done [cost:-0.65470==>-0.66315 ; 8 patches optimized, 0 skipped]
lev=2 patch=125x149x123 [clock= 11m 54s 659ms]..................... done [cost:-0.66315==>-0.70298 ; 21 patches optimized, 6 skipped]
lev=3 patch=95x111x91 [clock= 13m 27s 936ms]............:[cost=-0.75457]:........... done [cost:-0.70298==>-0.77280 ; 78 patches optimized, 50 skipped]
lev=4 patch=71x83x69 [clock= 18m 52s 458ms].........:[cost=-0.81939]:............... done [cost:-0.77280==>-0.83435 ; 164 patches optimized, 86 skipped]
lev=5 patch=53x63x51 [clock= 23m 53s 87ms]............:[cost=-0.88922]:............. done [cost:-0.83435==>-0.89404 ; 405 patches optimized, 281 skipped]
++ ========== total number of parameters 'optimized' = 8271
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5_AWARP.nii
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5.nii
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5_WARP.nii
++ Inverting warp ********.............:..
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5_WARPINV.nii
++ ===== clock time = 28m 46s 647ms
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 2 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2117569 survived, 6412452 were zero
++ writing result junk.SSwarper.LZXoki1Shmg_MASK.nii...
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_MASK.nii
++ 3dcalc: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5mm.nii
++ 3dNwarpApply: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is '/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatS.s2000.nii'
** AFNI converts NIFTI_datatype=2 (UINT8) in file /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5mm.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ opened source dataset '/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5mm.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5ww.nii
++ total Elapsed time = 20.6 sec
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 3 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2237335 survived, 6292686 were zero
++ writing result junk.SSwarper.LZXoki1Shmg_MASK.nii...
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_MASK.nii
++ 3dNwarpApply: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Zhark the Warped
++ -master dataset is '/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatS.s2000.nii'
++ opened source dataset '/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_MASK.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_MASKO.nii
++ total Elapsed time = 17.2 sec
++ 3dcalc: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: A cast of thousands
** ERROR: output dataset name 'anatSS.s2000.nii' conflicts with existing file
** ERROR: dataset NOT written to disk!
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 1394268 survived, 11188644 were zero
++ writing result junk.SSwarper.LZXoki1Shmg_de3.nii...
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_de3.nii
++ 3dcalc: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatSSc.s2000.nii
++ 3dAutomask: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Emperor Zhark
++ Loading dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatSSc.s2000.nii
++ Forming automask
+ Fixed clip level = 445.854980
+ Used gradual clip level = 437.293640 .. 452.464722
+ Number voxels above clip level = 1341614
+ Clustering voxels ...
+ Largest cluster has 1341456 voxels
+ Clustering voxels ...
+ Largest cluster has 1337210 voxels
+ Filled 17497 voxels in small holes; now have 1354707 voxels
+ Filled 41096 voxels in large holes; now have 1395803 voxels
+ Clustering voxels ...
+ Largest cluster has 1395803 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 11187109 voxels
+ Mask now has 1395803 voxels
++ 1395803 voxels in the mask [out of 12582912: 11.09%]
++ first 48 x-planes are zero [from A]
++ last 49 x-planes are zero [from P]
++ first 70 y-planes are zero [from S]
++ last 50 y-planes are zero [from I]
++ first 25 z-planes are zero [from R]
++ last 27 z-planes are zero [from L]
++ applying mask to original data
++ Writing masked data
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatSSd.s2000.nii
++ CPU time = 0.000000 sec
++ 3dAllineate: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Zhark the Registrator
** AFNI converts NIFTI_datatype=2 (UINT8) in file /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_TAL5mm.nii to FLOAT32
Warnings of this type will be muted for this session.
Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ Source dataset: /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatSS.s2000.nii
++ Base dataset: (not given)
++ Loading datasets
++ OpenMP thread count = 8
++ ========== Applying transformation to 1 sub-bricks ==========
++ wsinc5 interpolation setup:
+ taper function = Min sidelobe 3 term
+ taper cut point = 0.000
+ window radius = 5 voxels
+ window shape = Cubical
+ The above can be altered via the AFNI_WSINC5_* environment variables.
+ (To avoid this message, 'setenv AFNI_WSINC5_SILENT YES'.)
+ wsinc5 CUBE(5) mask has 1000 points
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_AffSS.nii
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 8.0
++ ###########################################################
++ OpenMP thread count = 8
++ 3dQwarp: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=21 xtop=20 ybot=15 ytop=24 zbot=21 ztop=15 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_AffSS.nii
++ AFNI warpomatic: 234 x 268 x 229 volume ; autobbox = 40..194 35..225 22..185 [clock= 11s 427ms]
lev=1 patch=145x177x153 [clock= 14s 922ms][first cost=-1.78583] . done [cost:-1.78583==>-1.81202 ; 1 patches optimized, 7 skipped]
lev=2 patch=109x133x115 [clock= 26s 463ms][first cost=-1.61987] ................ done [cost:-1.81202==>-1.70748 ; 16 patches optimized, 11 skipped]
lev=3 patch=81x99x87 [clock= 1m 30s 754ms][first cost=-1.34690] ........ done [cost:-1.70748==>-1.48777 ; 30 patches optimized, 34 skipped]
lev=4 patch=61x75x65 [clock= 3m 12s 387ms][first cost=-1.28207] .............. done [cost:-1.48777==>-1.35651 ; 77 patches optimized, 48 skipped]
lev=5 patch=45x57x49 [clock= 5m 6s 375ms][first cost=-1.21486] ..............:[cost=-1.28433]:............. done [cost:-1.35651==>-1.28737 ; 379 patches optimized, 307 skipped]
++ ========== total number of parameters 'optimized' = 6036
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_QQ5_WARP.nii
++ ===== clock time = 8m 41s 103ms
++ OpenMP thread count = 8
++ 3dQwarp: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=21 xtop=20 ybot=15 ytop=24 zbot=21 ztop=15 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_AffSS.nii
++ AFNI warpomatic: 234 x 268 x 229 volume ; autobbox = 40..194 35..225 22..185 [clock= 11s 317ms]
lev=6 patch=35x43x37 [clock= 12s 828ms][first cost=-1.20091] .......................:[cost=-1.25774]:................ done [cost:-1.20091==>-1.25419 ; 836 patches optimized, 622 skipped]
lev=7 patch=25x31x27 [clock= 3m 44s 59ms][first cost=-1.17410] ............................:[cost=-1.24364]:.......................................... done [cost:-1.25419==>-1.19086 ; 2271 patches optimized, 2123 skipped]
++ ========== total number of parameters 'optimized' = 37284
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_QQ7_WARP.nii
++ ===== clock time = 8m 21s 573ms
++ OpenMP thread count = 8
++ 3dQwarp: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=21 xtop=20 ybot=15 ytop=24 zbot=21 ztop=15 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_AffSS.nii
++ AFNI warpomatic: 234 x 268 x 229 volume ; autobbox = 40..194 35..225 22..185 [clock= 11s 428ms]
lev=8 patch=19x23x21 [clock= 12s 869ms][first cost=-1.20666] ....................................... done [cost:-1.20666==>-1.22471 ; 2505 patches optimized, 2119 skipped]
lev=9 patch=17x17x17 [clock= 3m 35s 436ms][first cost=-1.22193] .................................................................... done [cost:-1.22471==>-1.27943 ; 4748 patches optimized, 4828 skipped]
++ ========== total number of parameters 'optimized' = 87036
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_QQ9_WARP.nii
++ ===== clock time = 8m 40s 226ms
++ OpenMP thread count = 8
++ 3dQwarp: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=21 xtop=20 ybot=15 ytop=24 zbot=21 ztop=15 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/19.2.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_AffSS.nii
++ AFNI warpomatic: 234 x 268 x 229 volume ; autobbox = 40..194 35..225 22..185 [clock= 11s 297ms]
lev=10 patch=11x11x11 [clock= 12s 630ms][first cost=-1.26217] ................................................................................................................................................................. done [cost:-1.26217==>-1.25898 ; 18401 patches optimized, 20473 skipped]
++ ========== total number of parameters 'optimized' = 220812
** ERROR: output dataset name 'anatQQ.s2000.nii' conflicts with existing file
** ERROR: dataset NOT written to disk!
** ERROR: output dataset name 'anatQQ.s2000_WARP.nii' conflicts with existing file
** ERROR: dataset NOT written to disk!
++ ===== clock time = 14m 43s 609ms
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2014425 survived, 6515596 were zero
++ writing result junk.SSwarper.LZXoki1Shmg_de3.nii...
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.LZXoki1Shmg_de3.nii
++ 3dcalc: AFNI version=AFNI_19.2.04 (Jul 19 2019) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatQQc.s2000.nii
** ERROR: Xvfb -- not found in path -- @snapshot_volreg fails
** WARNING: this script cannot run without installing package netpbm11
** ERROR: Xvfb -- not found in path -- @snapshot_volreg fails
** WARNING: this script cannot run without installing package netpbm11
** warning: removing first 2 TRs from beginning of each run
--> the stimulus timing files must reflect the removal of these TRs
** WARNING: anat follower does not seem to exist: /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/s2000.nii
originally from /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/s2000.nii
** -tlrc_anat dataset '/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/anatSS.s2000.nii' does not exist
** invalid block : tlrc
----------------------------------------------------------------------
** failed command (create_blocks):

afni_proc.py -subj_id s2000 -script proc.script.s2000 -out_dir \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results \
-scr_overwrite -blocks despike tshift align tlrc volreg mask blur scale \
regress -radial_correlate_blocks tcat volreg -copy_anat \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/anatSS.s2000.nii \
-anat_follower anat_w_skull anat \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/s2000.nii \
-tcat_remove_first_trs 2 -dsets \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/epi/epi_r01+orig \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/epi/epi_r02+orig \
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -align_opts_aea \
-check_flip -cost lpc+zz -giant_move -AddEdge -blur_size 6 \
-blur_to_fwhm -anat_has_skull no -volreg_tlrc_warp -tlrc_base \
MNI152_2009_template_SSW.nii.gz -tlrc_NL_warp -tlrc_NL_warped_dsets \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/anatQQ.s2000.nii \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/anatQQ.s2000.aff12.1D \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/results/anat.SSwarper/anatQQ.s2000_WARP.nii \
-mask_epi_anat yes -regress_stim_times \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/stimuli/s2000__realcry_timing.1D \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/stimuli/s2000__controlcry_timing.1D \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/stimuli/s2000_realcrynoise_timing.1D \
/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/s2000/stimuli/s2000_controlnoise_timing.1D \
-regress_stim_labels realcry controlcry realcrynoise controlnoise \
-regress_basis 'BLOCK(20,1)' -regress_local_times \
-regress_motion_per_run -regress_censor_motion 0.5 \
-regress_censor_outliers 0.1 -regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D -regress_est_blur_epits \
-regress_est_blur_errts -regress_reml_exec -regress_compute_fitts \
-regress_opts_3dD -bout -jobs 12 -num_glt 1 -gltsym 'SYM: +realcry \
+controlcry +realcrynoise +controlnoise' -glt_label 1 PosControl \
-execute
----------------------------------------------------------------------
[lgrande2@node2 AFNI_scripts]$