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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
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
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
| July 02, 2020 05:01PM | |
Registered: 3 years ago Posts: 6 |
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]$
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]$
| Subject | Author | Posted |
|---|---|---|
|
leahariana | July 02, 2020 05:01PM |
|
ptaylor | July 06, 2020 07:38AM |
|
leahariana | July 14, 2020 02:51PM |
|
ptaylor | July 14, 2020 03:41PM |
|
leahariana | July 20, 2020 01:27AM |
|
ptaylor | July 20, 2020 02:36PM |
|
leahariana | July 20, 2020 10:38PM |
|
ptaylor | July 22, 2020 09:43AM |
|
ptaylor | July 24, 2020 02:06PM |
