AFNI preprocessing help

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1

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]$

2

Hi, Leah-

What is the output of:


which Xvfb

?

Also, could we please see the output of:


afni_system_check.py -check_all

?

That last command will tell us what operating system that you are using, which I am not of at present (presumably some form of Linux). I assume that you gave your IT folks the pointer to the AFNI setup instructions at some point?
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/main_toc.html

–pt

3

Here is the output of which Xvfb:
lgrande2@node2 AFNI_scripts]$ which Xvfb
/usr/bin/which: no Xvfb in (/usr/local/netpbm/10.73.32/bin:/usr/local/R/3.3.3/bin:/usr/local/gdal/2.1.3/bin:/usr/local/proj/4.9.3/bin:/usr/local/curl/7.53.1/bin:/usr/local/geos/3.6.1/bin:/usr/local/openmpi/1.10.6/gnu/4.8.5-rhel/ib/bin:/usr/local/afni/19.2.04:/usr/local/R/3.6.1/bin:/usr/local/curl/7.64.1/bin:/usr/local/proj/6.0.0/bin:/usr/local/jags/4.3.0/bin:/usr/local/gdal/2.4.1/bin:/usr/local/geos/3.7.1/bin:/usr/local/udunits2/2.2.26/bin:/usr/local/gsl/2.5/bin:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/bin:/usr/local/gcc/8.3.0/bin:/usr/local/Modules/3.2.10/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/lgrande2/bin)

Here is the output of: afni_system_check.py -check_all
[i][lgrande2@node2 AFNI_scripts]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1062.9.1.el7.x86_64
version: #1 SMP Mon Dec 2 08:31:54 EST 2019
distribution: Red Hat Enterprise Linux Server 7.7 Maipo
number of CPUs: 8
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/19.2.04/afni
afni version : Precompiled binary linux_openmp_64: Jul 19 2019
: AFNI_19.2.04 ‘Claudius’
AFNI_version.txt : AFNI_19.2.04, linux_openmp_64, Jul 19 2019
which python : /usr/bin/python
python version : 2.7.5
which R : /usr/local/R/3.3.3/bin/R
R version : R version 3.3.3 (2017-03-06) – “Another Canoe”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/afni/19.2.04/afni)
R : 2
/usr/local/R/3.3.3/bin/R
/usr/local/R/3.6.1/bin/R
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 0

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE

    oo Warning: 
       These packages are not installed on the computer: afex!
    These packages are not installed on the computer: paran!
    These packages are not installed on the computer: psych!
    These packages are not installed on the computer: corrplot!
    These packages are not installed on the computer: metafor!

checking for $HOME files…
.afnirc : missing
.sumarc : missing
.afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
++ module ‘PyQt4’ found at /usr/lib64/python2.7/site-packages/PyQt4
++ module loaded: PyQt4

-------------------------------- env vars --------------------------------
PATH = /usr/local/netpbm/10.73.32/bin:/usr/local/R/3.3.3/bin:/usr/local/gdal/2.1.3/bin:/usr/local/proj/4.9.3/bin:/usr/local/curl/7.53.1/bin:/usr/local/geos/3.6.1/bin:/usr/local/openmpi/1.10.6/gnu/4.8.5-rhel/ib/bin:/usr/local/afni/19.2.04:/usr/local/R/3.6.1/bin:/usr/local/curl/7.64.1/bin:/usr/local/proj/6.0.0/bin:/usr/local/jags/4.3.0/bin:/usr/local/gdal/2.4.1/bin:/usr/local/geos/3.7.1/bin:/usr/local/udunits2/2.2.26/bin:/usr/local/gsl/2.5/bin:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/bin:/usr/local/gcc/8.3.0/bin:/usr/local/Modules/3.2.10/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/home/lgrande2/bin

PYTHONPATH = /usr/lib64/python2.7

R_LIBS =
LD_LIBRARY_PATH = /usr/local/netpbm/10.73.32/lib:/usr/local/R/3.3.3/lib64:/usr/local/gdal/2.1.3/lib:/usr/local/proj/4.9.3/lib:/usr/local/curl/7.53.1/lib:/usr/local/lapack/3.7.0/lib:/usr/local/blas/3.7.0/lib:/usr/local/geos/3.6.1/lib:/usr/local/openmpi/1.10.6/gnu/4.8.5-rhel/ib/lib:/usr/local/afni/19.2.04:/usr/local/R/3.6.1/lib64:/usr/local/curl/7.64.1/lib:/usr/local/proj/6.0.0/lib:/usr/local/jags/4.3.0/lib:/usr/local/gdal/2.4.1/lib:/usr/local/geos/3.7.1/lib:/usr/local/udunits2/2.2.26/lib:/usr/local/gsl/2.5/lib:/usr/local/lapack/3.8.0/lib64:/usr/local/blas/3.8.0/lib:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/lib:/usr/local/gcc/8.3.0/lib64:/opt2/amd-opencl/lib

DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: … [rickr]: updated FT_white.nii w/out 16 (brain stem)
data dir : found AFNI_demos under $HOME
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /usr/local/afni/19.2.04

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3

========================= summary, please fix: =========================

  • login shell ‘bash’, trusting user to translate code examples from ‘tcsh’
  • shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
  • missing R packages (see rPkgsInstall)
  • please run: cp /usr/local/afni/19.2.04/AFNI.afnirc ~/.afnirc
  • please run: “suma -update_env” for .sumarc
  • please run: apsearch -update_all_afni_help[/i]

I will share the AFNI setup instructions with the IT folks. I am sure we gave it to them in the past, but it would be good to share again as the IT person may be different now.

Thank you for your help!

-Leah

4

Hi, Leah-

The output of “which Xvfb” demonstrates that that program is not currently installed on that system. From the afni_system_check.py output, your system appears to be Red Hat Linux, so you can please pass along this page of install instructions to your IT folks:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_Fed_RH.html
… in particular, the dependency list for Red Hat in this section:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_Fed_RH.html#install-prerequisite-packages
… which includes “Xvfb” (but they should proabbly just copy+paste that whole chunk).

But they should probably go through the R install stuff, too, it appears. Note that you will really want the R-3.6.* version to be your main one-- R-3.3.* is suuuuper old and won’t have the necessary capabilities for running any of AFNI’s R-dependent programs.

Also, this output of the afni_system_check.py shows that your version of AFNI is quite old-- just about coming up on its one year birthday!:


afni version : Precompiled binary linux_openmp_64: Jul 19 2019

… so you should ask your IT to run:


@update.afni.binaries -d

to update it.

… And please see the things that you can do for helping your AFNI setup (sudo password not required), as listed in the bottom of the afni_system_check.py output. You can copy+paste each of these into the terminal:

For: * shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile


echo "" >> ~/.bash_profile
echo "source ~/.bashrc" >> ~/.bash_profile
echo "" >> ~/.bash_profile

For: * please run: cp /usr/local/afni/19.2.04/AFNI.afnirc ~/.afnirc


cp /usr/local/afni/19.2.04/AFNI.afnirc ~/.afnirc

For: * please run: “suma -update_env” for .sumarc


suma -update_env

For: * please run: apsearch -update_all_afni_help


apsearch -update_all_afni_help

–pt

5

Thank you so much for your help! I talked with IT to update the programs. I also used the commands you sent to help with the AFNI setup. I believe the programs should be good now, bu let me know if something looks wrong and I can talk with IT again.

I am getting a few different errors now with my script. Would you be able to take a look and let me know what might be the issue? I am including the output and the script below.

Thank you!

Best,
Leah

Here is my output:
[lgrande2@du-hpc ~]$ ssh -X node37
Last login: Tue Jun 30 12:19:42 2020 from du-hpc
[lgrande2@node37 ~]$ module load apps/afni-20.04
[lgrande2@node37 ~]$ module load apps/R-4.0.2
[lgrande2@node37 ~]$ module load tools/netpbm-10.73.32
[lgrande2@node37 ~]$
[lgrande2@node37 ~]$ module load tools/netpbm-10.73.32
[lgrande2@node37 ~]$ cd /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/scripts/AFNI_scripts
[lgrande2@node37 AFNI_scripts]$ tcsh afni_proc_Leah_SSwarper_7.14.20
++ Starting: @SSwarper v2.2
++ Default OMP_NUM_THREADS is 16
ParseName: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
ParseName: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
++ SSW Step 1
*+ 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.
++ 3dcalc: AFNI version=AFNI_20.2.02 (Jul 12 2020) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUAC.s2000.nii
++ SSW Step 2
++ SSW Step 3
++ OpenMP thread count = 15

+++ Command Echo:
3dQwarp -lite -base /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz[1] -lpa -warpscale 1 -source /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUAC.s2000.nii -weight /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz[2] -allineate -noneg -maxlev 5 -iwarp -awarp -wtgaus 4.5 -inedge -workhard:3:5 -nopenalty -prefix /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5.nii

++ 3dQwarp: AFNI version=AFNI_20.2.02 (Jul 12 2020) [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/anatUAC.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/anatUAC.s2000.nii is 2.861839 degrees from plumb.
++ ###############################################################

  • Starting 3dAllineate (affine register) command:

3dAllineate -base /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz[1] -source /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUAC.s2000.nii -prefix /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_Allin.nii -1Dmatrix_save /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_Allin -cmass -final wsinc5 -float -master BASE -twobest 7 -weight /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz[2] -zclip -cost lpa+ZZ -fineblur 4.44

  • ###############################################################
    ++ 3dAllineate: AFNI version=AFNI_20.2.02 (Jul 12 2020) [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/anatUAC.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/anatUAC.s2000.nii is 2.861839 degrees from plumb.
    ++ lpa+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
    *+ WARNING: ‘-source_automask’ is strongly recommended when using -lpc or -lpa
    ++ Source dataset: /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatUAC.s2000.nii
    ++ Base dataset: /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz
    ++ Loading datasets into memory
    ++ 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.

++ Local correlation: blok type = ‘RHDD(6.54321)’
++ lpa+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
++ OpenMP thread count = 15
++ ======= Allineation of 1 sub-bricks using Local Pearson Abs + Others =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***

  • Final fine fit Parameters:
    x-shift= -7.9645 y-shift=-17.2154 z-shift= 0.9511 … enorm= 18.9923 mm
    z-angle= -0.7239 x-angle= 17.1055 y-angle= 1.2056 … total= 17.1552 deg
    x-scale= 0.9548 y-scale= 0.8727 z-scale= 0.8367 … vol3D= 0.6972 = base bigger than source
    y/x-shear= -0.0024 z/x-shear= -0.0120 z/y-shear= -0.0709
    ++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_Allin.nii
    ++ Wrote -1Dmatrix_save /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_Allin.aff12.1D
    ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 2535.9
    ++ ###########################################################
    ++ # Please check results visually for alignment quality #
    ++ ###########################################################
    ++ # ‘-autoweight’ is recommended when using -lpc or -lpa #
    ++ # If your results are not good, please try again. #
    ++ ###########################################################

++ 3dQwarp: replacing source dataset with 3dAllineate result /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_Allin.nii

mat44 3dAllineate matrix:

  0.954624     -0.006153     -0.019201      -7.964460
  0.008287      0.834038      0.256733     -17.215401
  0.002280     -0.305263      0.781533       0.951096

++ Dataset zero-pad: xbot=15 xtop=14 ybot=13 ytop=22 zbot=15 ztop=9 voxels
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_Allin.nii
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 43m 15s 140ms]
lev=0 0…221 0…263 0…216: [first cost=-2.27810] … done [cost:-2.27810==>-2.96326]
lev=1 patch=167x197x163 [clock= 47m 25s 667ms]… done [cost:-2.96326==>-6.97825 ; 8 patches optimized, 0 skipped]
lev=2 patch=125x149x123 [clock= 48m 21s 581ms]… done [cost:-6.97825==>-5.86694 ; 25 patches optimized, 2 skipped]
lev=3 patch=93x111x91 [clock= 50m 15s 412ms]…:[cost=-5.66432]:… done [cost:-5.86694==>-5.87136 ; 84 patches optimized, 44 skipped]
lev=4 patch=71x83x69 [clock= 53m 34s 35ms]…:[cost=-5.23055]:… done [cost:-5.87136==>-5.25828 ; 164 patches optimized, 86 skipped]
lev=5 patch=53x63x51 [clock= 57m 30s 524ms]…:[cost=-5.43163]:… done [cost:-5.25828==>-5.86742 ; 405 patches optimized, 281 skipped]
++ ====== total number of parameters ‘optimized’ = 8379

  •  initial unpenalized cost = -2.2781

  •    final unpenalized cost = -5.86742

  •    final penalized   cost = -5.86742

++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_AWARP.nii
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5.nii
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_WARP.nii
++ Inverting warp ********…:…
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_WARPINV.nii
++ ===== clock time = 1h 4m 14s 761ms
++ SSW Step 4
++ no -frac option: defaulting to -union
++ processing 1 input dataset(s), NN=2…
++ 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.EanCOAEvWf8_MASK.nii…
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_MASK.nii
++ 3dcalc: AFNI version=AFNI_20.2.02 (Jul 12 2020) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5mm.nii
++ SSW Step 5

+++ Command Echo:
3dNwarpApply -nwarp /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_WARPINV.nii -master /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatS.s2000.nii -source /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5mm.nii -prefix /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5ww.nii

++ 3dNwarpApply: AFNI version=AFNI_20.2.02 (Jul 12 2020) [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.EanCOAEvWf8_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.EanCOAEvWf8_TAL5mm.nii’
++ Processing -nwarp
++ Warping:.Z
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5ww.nii
++ total Elapsed time = 16.3 sec

+++ Command Echo:
3dmask_tool -input /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz[3] -dilate_input 3 -prefix /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_MASK.nii

++ no -frac option: defaulting to -union
++ processing 1 input dataset(s), NN=2…
++ 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.EanCOAEvWf8_MASK.nii…
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_MASK.nii
++ 3dNwarpApply: AFNI version=AFNI_20.2.02 (Jul 12 2020) [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.EanCOAEvWf8_MASK.nii’
++ Processing -nwarp
++ Warping:.Z
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_MASKO.nii
++ total Elapsed time = 13.1 sec
++ 3dcalc: AFNI version=AFNI_20.2.02 (Jul 12 2020) [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 dataset(s), NN=2…
++ padding all datasets by 0 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 1394059 survived, 11188853 were zero
++ writing result junk.SSwarper.EanCOAEvWf8_de3.nii…
++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_de3.nii
++ 3dcalc: AFNI version=AFNI_20.2.02 (Jul 12 2020) [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_20.2.02 (Jul 12 2020) [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 = 1341488
  • Clustering voxels …
  • Largest cluster has 1341330 voxels
  • Clustering voxels …
  • Largest cluster has 1337090 voxels
  • Filled 17484 voxels in small holes; now have 1354574 voxels
  • Filled 41045 voxels in large holes; now have 1395619 voxels
  • Clustering voxels …
  • Largest cluster has 1395619 voxels
  • Clustering non-brain voxels …
  • Clustering voxels …
  • Largest cluster has 11187293 voxels
  • Mask now has 1395619 voxels
    ++ 1395619 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
    ++ SSW Step 6
    ++ SSW Step 6 … piece 0
    ++ 3dAllineate: AFNI version=AFNI_20.2.02 (Jul 12 2020) [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.EanCOAEvWf8_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.
    ++ lpa+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
    ++ Source dataset: /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatSS.s2000.nii
    ++ Base dataset: (not given)
    ++ Loading datasets into memory
    ++ Local correlation: blok type = ‘RHDD(6.54321)’
    ++ lpa+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40 [to be zeroed at Final iteration]
  •    -cmass x y z shifts =    0.000    0.000    0.000
  • shift search range is +/- = 61.311 81.855 81.855
    ++ OpenMP thread count = 15
    ++ ========== 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.EanCOAEvWf8_AffSS.nii
    ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 6.4
    ++ ###########################################################
    ++ SSW Step 6 … piece 1
    ++ OpenMP thread count = 15

+++ Command Echo:
3dQwarp -lite -base /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz[0] -source /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_AffSS.nii -iniwarp /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_TAL5_AWARP.nii -warpscale 1 -lpa -inilev 1 -maxlev 5 -wtgaus 4.5 -inedge -pblur -workhard:5:5 -nodset -prefix /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_QQ5.nii

++ 3dQwarp: AFNI version=AFNI_20.2.02 (Jul 12 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=15 xtop=14 ybot=13 ytop=22 zbot=15 ztop=9 voxels
++ Weightizing the base image: FWHM = 4.5 (vox)
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_AffSS.nii
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 36s 776ms]
lev=1 patch=145x177x149 [clock= 39s 545ms][first cost=-17.53411] … done [cost:-17.53411==>-16.97129 ; 3 patches optimized, 5 skipped]
lev=2 patch=109x133x113 [clock= 53s 879ms][first cost=-14.98542] … done [cost:-16.97129==>-15.02939 ; 17 patches optimized, 10 skipped]
lev=3 patch=81x99x85 [clock= 1m 35s 186ms][first cost=-11.39344] … done [cost:-15.02939==>-12.74408 ; 34 patches optimized, 30 skipped]
lev=4 patch=61x75x63 [clock= 3m 17s 538ms][first cost=-8.64879] … done [cost:-12.74408==>-10.41111 ; 78 patches optimized, 47 skipped]
lev=5 patch=45x57x47 [clock= 5m 57s 953ms][first cost=-7.96615] …:[cost=-9.63238]:… done [cost:-10.41111==>-10.08320 ; 386 patches optimized, 300 skipped]
++ ====== total number of parameters ‘optimized’ = 6216

  •  initial unpenalized cost = -17.5341

  •    final unpenalized cost = -10.754

  •    final penalized   cost = -10.0832

++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_QQ5_WARP.nii
++ ===== clock time = 16m 22s 655ms
++ SSW Step 6 … piece 2
++ OpenMP thread count = 15

+++ Command Echo:
3dQwarp -lite -base /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz[0] -source /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_AffSS.nii -iniwarp /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_QQ5_WARP.nii -warpscale 1 -pcl -inilev 6 -maxlev 7 -workhard:6:7 -wtgaus 4.5 -inedge -pblur -nodset -prefix /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_QQ7.nii

++ 3dQwarp: AFNI version=AFNI_20.2.02 (Jul 12 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=15 xtop=14 ybot=13 ytop=22 zbot=15 ztop=9 voxels
++ Weightizing the base image: FWHM = 4.5 (vox)
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_AffSS.nii
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 37s 309ms]
lev=6 patch=35x43x35 [clock= 38s 440ms][first cost=-0.72291] …:[cost=-0.97294]:… done [cost:-0.72291==>-1.04292 ; 883 patches optimized, 737 skipped]
lev=7 patch=25x31x27 [clock= 39m 17s 286ms][first cost=-0.88036] …:[cost=-0.97945]:… done [cost:-1.04292==>-1.02005 ; 2271 patches optimized, 2123 skipped]
++ ====== total number of parameters ‘optimized’ = 37848

  •  initial unpenalized cost = -1.12034

  •    final unpenalized cost = -1.36723

  •    final penalized   cost = -1.02005

++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_QQ7_WARP.nii
++ ===== clock time = 2h 9m 20s 66ms
++ SSW Step 6 … piece 3a
++ OpenMP thread count = 15

+++ Command Echo:
3dQwarp -lite -base /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz[0] -source /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_AffSS.nii -iniwarp /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_QQ7_WARP.nii -warpscale 1 -pcl -inilev 8 -minpatch 17 -wtgaus 4.5 -inedge -pblur -nodset -prefix /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_QQ9.nii

++ 3dQwarp: AFNI version=AFNI_20.2.02 (Jul 12 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=15 xtop=14 ybot=13 ytop=22 zbot=15 ztop=9 voxels
++ Weightizing the base image: FWHM = 4.5 (vox)
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_AffSS.nii
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 37s 288ms]
lev=8 patch=19x23x21 [clock= 38s 358ms][first cost=-1.04273] … done [cost:-1.04273==>-1.10207 ; 2505 patches optimized, 2119 skipped]
lev=9 patch=17x17x17 [clock= 1h 36m 25s 85ms][first cost=-1.00016] … done [cost:-1.10207==>-1.05347 ; 4747 patches optimized, 4829 skipped]
++ ====== total number of parameters ‘optimized’ = 87024

  •  initial unpenalized cost = -1.31893

  •    final unpenalized cost = -1.40326

  •    final penalized   cost = -1.05347

++ Output dataset /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_QQ9_WARP.nii
++ ===== clock time = 4h 27m 7s 145ms
++ SSW Step 6 … piece 3b
++ OpenMP thread count = 15

+++ Command Echo:
3dQwarp -lite -base /usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz[0] -source /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_AffSS.nii -iniwarp /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_QQ9_WARP.nii -warpscale 1 -pcl -inilev 10 -wtgaus 4.5 -inedge -pblur -minpatch 11 -prefix /data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/anatQQ.s2000.nii

++ 3dQwarp: AFNI version=AFNI_20.2.02 (Jul 12 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=15 xtop=14 ybot=13 ytop=22 zbot=15 ztop=9 voxels
++ Weightizing the base image: FWHM = 4.5 (vox)
++ +++++++++++ Begin warp optimization: base=/usr/local/afni/20.04/MNI152_2009_template_SSW.nii.gz source=/data2/psychology/kimlab/fmri/studies/IDEA/infantcry/Leah/data/anat.SSwarper/junk.SSwarper.EanCOAEvWf8_AffSS.nii
^C
Fatal Signal 2 (SIGINT) received
Last STATUS: call Extract_Gradient_Maxima_3D
mri_interior_edgeize
IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
Bottom of Debug Stack
** AFNI version = AFNI_20.2.02 Compile date = Jul 12 2020
** [[Precompiled binary linux_centos_7_64: Jul 12 2020]]
** Program Death **

Here is my script (I’m just running SSwarper right now):

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

6

Hi, Leah-

What is the output of


afni_system_check.py -check_all

on that system?

Also, note that it won’t matter for this command, but at the moment you want to use R-3.6.[something], not R-4.[something].

–pt

7

Thank you! Here you go:

lgrande2@du-hpc ~]$ ssh -X node37
Last login: Sun Jul 19 15:00:27 2020 from du-hpc
[lgrande2@node37 ~]$ module load apps/afni-20.04
[lgrande2@node37 ~]$ module load apps/R-3.6.1
[lgrande2@node37 ~]$
[lgrande2@node37 ~]$ module load tools/netpbm-10.73.32
[lgrande2@node37 ~]$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-1062.9.1.el7.x86_64
version: #1 SMP Mon Dec 2 08:31:54 EST 2019
distribution: Red Hat Enterprise Linux Server 7.7 Maipo
number of CPUs: 16
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /usr/local/afni/20.04/afni
afni version : Precompiled binary linux_centos_7_64: Jul 12 2020
: AFNI_20.2.02 ‘Aulus Vitellius’
AFNI_version.txt : AFNI_20.2.02, linux_centos_7_64, Jul 12 2020
which python : /usr/bin/python
python version : 2.7.5
which R : /usr/local/R/3.6.1/bin/R
R version : R version 3.6.1 (2019-07-05) – “Action of the Toes”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/usr/local/afni/20.04/afni)
R : 1 (/usr/local/R/3.6.1/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.6)

testing ability to start various programs…
afni : success
suma : FAILURE
suma: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : FAILURE
SurfMesh: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory
3dClustSim : success
3dMVM : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : success

R RHOME : /usr/local/R/3.6.1/lib64/R

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib64/python2.7/site-packages/PyQt4/init.pyc

** failed to load module matplotlib.pyplot
– matplotlib.pyplot is not required, but is desirable

-------------------------------- env vars --------------------------------
PATH = /usr/local/netpbm/10.73.32/bin:/usr/local/afni/20.04:/usr/local/R/3.6.1/bin:/usr/local/curl/7.64.1/bin:/usr/local/proj/6.0.0/bin:/usr/local/jags/4.3.0/bin:/usr/local/gdal/2.4.1/bin:/usr/local/geos/3.7.1/bin:/usr/local/udunits2/2.2.26/bin:/usr/local/gsl/2.5/bin:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/bin:/usr/local/gcc/8.3.0/bin:/usr/local/Modules/3.2.10/bin:/opt/sge/bin:/opt/sge/bin/lx-amd64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/lgrande2/bin

PYTHONPATH =
R_LIBS =
LD_LIBRARY_PATH = /usr/local/netpbm/10.73.32/lib:/usr/local/afni/20.04:/usr/local/R/3.6.1/lib64:/usr/local/curl/7.64.1/lib:/usr/local/proj/6.0.0/lib:/usr/local/jags/4.3.0/lib:/usr/local/gdal/2.4.1/lib:/usr/local/geos/3.7.1/lib:/usr/local/udunits2/2.2.26/lib:/usr/local/gsl/2.5/lib:/usr/local/lapack/3.8.0/lib64:/usr/local/blas/3.8.0/lib:/usr/local/openmpi/4.0.1/ib-gcc8.3.0/lib:/usr/local/gcc/8.3.0/lib64:/opt2/amd-opencl/lib

DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: … [rickr]: updated FT_white.nii w/out 16 (brain stem)
data dir : found AFNI_demos under $HOME
top history: … [pault]: remove rank from FATCAT_DEMO, FAT_MVM_DEMO
data dir : found suma_demo under $HOME
top history: …/SUMA_data/Build_tmp on Wed Aug 20 10:04:23 EDT 2014
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /usr/local/afni/20.04

------------------------------ OS specific -------------------------------
which yum : /usr/bin/yum
yum version : 3.4.3

========================= summary, please fix: =========================

  • just be aware: login shell ‘bash’, but our code examples use ‘tcsh’
  • AFNI programs show FAILURE

[lgrande2@node37 ~]$

8

Hi, Leah-

There is still a dependency missing as part of your system’s setup-- this is something your system administrators need to sort out.

In particular, the missing library is pointed out in this kind of error message in the system check:


suma: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory

… which means that a library called “mesa” is missing, I believe. (It is possible it comes as part of the “epel-release” dependency that we install on most systems, since I don’t see an explicit library for that in the RedHat 7 installation instructions for AFNI.)

Can you ask your admin to install that package? It might be done with something like “sudo yum install -y mesa-libGLw”, but I don’t have a RedHat 7 system to test on at the moment…

Your administrators can run the “afni_system_check.py -check_all” just like you did, and see if the dependency is resolved.

–pt

9

Hi-

… and I now have access to a CentOS system and have found that I need to add the following to the install instructions (which will soon be updated in the online install pages):


sudo yum install -y   mesa-libGLw mesa-libGLU

… because I had been getting error messages:


suma: error while loading shared libraries: libGLw.so.1: cannot open shared object file: No such file or directory



suma: error while loading shared libraries: libGLU.so.1: cannot open shared object file: No such file or directory

Hope that helps-- sorry for the hassle.

–pt