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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 20, 2020 01:27AM | |
Registered: 3 years ago Posts: 6 |
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 ${out_dir}/anat.SSwarper
I am getting a few different errors now with my script. Would you be able to take a look and let me know what might be the issue? I am including the output and the script below.
Thank you!
Best,
Leah
Here is my output:
[lgrande2@du-hpc ~]$ 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
| 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 |
