Hello AFNI,

I was hoping to get some clarification on the appropriate @SSwarper code I should be using.

I have been using the following code to run the @SSwarper:
@SSwarper \
11987.anat+orig \
MNI152_2009_template.nii.g \
11987

However, upon corresponding with an AFNI gurus, I realized that I was running the old @SSwarper and that I could run the following code instead, so that my outputs had my subject ID in them
@SSwarper \
11987.anat+orig \
11987

I have noticed that when I run the "old" code, it seems to get stuck on during the "warp optimization" section and continues to runs for hours, even days (see the output below). However, when I run the "new" code, it seems to run successfully. Is there a reason why both codes are not working? Is it "okay" if I use the "old" code to run @SSwarper?

Thank you in advance for your help.

Best,
Tamara


Terminal Output of "new" code

-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /usr/local/freesurfer
FSFAST_HOME /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /home/bmiadmin/subjects
MNI_DIR /usr/local/freesurfer/mni
SUBJECTS_DIR= /home/bmiadmin/subjects
mitchelllab-linux:~/Tamara/PRR_Analysis/11987> @SSwarper \
? 11987.anat+orig \
? 11987
SUBJECTS_DIR= /home/bmiadmin/subjects
++ 3dUnifize: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./11987.anat+orig.BRIK,
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:./11987.anat+orig.BRIK is 0.142653 degrees from plumb.
+ Pre-processing: ADV................UWG
++ Output dataset ./anatU.11987.nii
++ ===== Elapsed = 24.7 sec
++ Notice SUMA_BrainWrap_ParseInput (SUMA_3dSkullStrip.c:1219 @09:37:38):
Setting fill_hole to 10
++ Notice 3dSkullStrip (SUMA_3dSkullStrip.c:1529 @09:37:38):
Loading dset, performing Spatial Normalization
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as anatU.11987.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:anatU.11987.nii is 0.142653 degrees from plumb.
3dSkullStrip:
Original resolution 1.000002, -1.000002, 1.000003
SpatNorm resolution 1.000002, 1.000002, 1.000003
++mri_brainormalize: normalizing
++mri_brainormalize: top clip above slice 254
++mri_brainormalize: bot clip below slice 84
++mri_brainormalize: Rescaling.
++mri_brainormalize: Eroding, clustering ...
+ Eroded 362572 voxels
+ Restored 300359 eroded voxels
+ Clustering voxels ...
+ Largest cluster has 3188439 voxels
+ Clustering voxels ...
+ Largest cluster has 2979588 voxels
++mri_brainormalize: Clipping extreme values.
+ scaling by fac=0.0524691
3dSkullStrip: -spatnorm: Expecting 6195700 voxels in in_vol dset (167 212 175)
3dSkullStrip: Edge threshold set to 47.128998. (minimum acceptable was 22.842131)
(92.000000 percentile =47.128998, 99.999001 percentile = 228.421310)
3dSkullStrip: Prepping volume...
SUMA_LoadPrepInVol: Volume 3213642.000000, radius 91.545380
3dSkullStrip: Beginning brain extraction...
3dSkullStrip: Have surface, OK for 1st entry.
3dSkullStrip: Stretching to avoid ventricles.
SO->Center is [1.055698 16.702696 -12.525011]
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, low MaxExp
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 3650 troubled nodes, going for more...
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, low MaxExp
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.100822 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: pastarea = 79507.312004
SUMA_StretchToFitLeCerveau:
Stage1: MaxExp = 0.683446, darea = 0.000000, going for more...
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.086837 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.025359 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.039028 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.014250 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
reducing tightness, applying touchup with Stage2Type = 1
SUMA_StretchToFitLeCerveau:
Stage 2, type 1: 0.000723 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Stage converged. Moving to new Stage or Type.
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: satiated, small area differential.
SUMA_StretchToFitLeCerveau:
Stage 3, type 2: 1.000000 change in troubled nodes.
SUMA_StretchToFitLeCerveau:
Continuing with Stage.
3dSkullStrip: Checking for self intersection...
3dSkullStrip: No intersections found.
3dSkullStrip: Final smoothing of 72
3dSkullStrip: Touchup correction, pass 1 ...
3dSkullStrip: The beauty treatment smoothing.
3dSkullStrip: Locating voxels inside surface ...
3dSkullStrip: Setting output to orig_vol (iset = 0x2f67ce8) (osnd = 0x413ddc8)...
3dSkullStrip: Coercing...
3dSkullStrip: Writing masked volume ...
3dSkullStrip: Applying a bit of erosion and dilatation
++ OpenMP thread count = 8
++ 3dQwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as anatU.11987.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:anatU.11987.nii is 0.142653 degrees from plumb.
++ Starting 3dAllineate (affine register) command:
3dAllineate -base /home/bmiadmin/abin/MNI152_2009_template.nii.gz[1] -source anatU.11987.nii -prefix AFN_kM6n_IUyylrRJpsHJNwNFg.nii -1Dmatrix_save AFN_kM6n_IUyylrRJpsHJNwNFg -cmass -final wsinc5 -float -master BASE -twobest 7 -zclip -fineblur 4.44

++ ###########################################################
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as anatU.11987.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:anatU.11987.nii is 0.142653 degrees from plumb.
++ Source dataset: ./anatU.11987.nii
++ Base dataset: /home/bmiadmin/abin/MNI152_2009_template.nii.gz
++ Loading datasets
++ 6527249 voxels in source_automask+0
++ Zero-pad: ybot=0 ytop=1
++ Computing -autobox
++ 8007930 voxels [93.5%] in weight mask
++ Number of points for matching = 3763727
++ NOTE: base and source coordinate systems have different handedness
+ Orientations: base=Right handed (LPI); source=Left handed (ASR)
++ OpenMP thread count = 8
++ ======= Allineation of 1 sub-bricks using Hellinger metric =======
++ *** Coarse pass begins ***
++ *** Fine pass begins ***
+ Final fine fit Parameters:
x-shift=-1.8165 y-shift=-20.5583 z-shift= 5.4606
z-angle= 1.1994 x-angle= 9.2621 y-angle= 2.9879
x-scale= 0.9036 y-scale= 0.9894 z-scale= 0.8789
y/x-shear= 0.0144 z/x-shear=-0.0205 z/y-shear=-0.0852
++ Output dataset ./AFN_kM6n_IUyylrRJpsHJNwNFg.nii
++ Wrote -1Dmatrix_save AFN_kM6n_IUyylrRJpsHJNwNFg.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 758.9
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################

++ 3dQwarp: replacing source dataset with 3dAllineate result junk.SSwarper.JLjQnJRzs5c_TAL5_Allin.nii
+ 3dAllineate output files have been renamed
# mat44 3dAllineate matrix:
0.901998 0.026467 -0.046485 -1.816440
-0.007442 0.976627 0.158569 -20.558300
0.031974 -0.224018 0.853645 5.460660
++ Dataset zero-pad: xbot=24 xtop=23 ybot=18 ytop=27 zbot=24 ztop=18 voxels
++ +++++++++++ Begin warp optimization: base=/home/bmiadmin/abin/MNI152_2009_template.nii.gz source=./junk.SSwarper.JLjQnJRzs5c_TAL5_Allin.nii
++ AFNI warpomatic: 240 x 274 x 235 volume ; autobbox = 30..209 31..243 30..204 [clock= 12m 41s 7ms]
lev=0 8..231 5..269 9..225: [first cost=-0.44210] .. done [cost:-0.44210==>-0.55226]
lev=1 patch=181x207x177 [clock= 15m 0s 173ms]........ done [cost:-0.55226==>-0.58763 ; 8 patches optimized, 0 skipped]
lev=2 patch=135x155x133 [clock= 22m 0s 790ms]..................... done [cost:-0.58763==>-0.65361 ; 21 patches optimized, 6 skipped]
lev=3 patch=101x117x99 [clock= 30m 44s 764ms]............ done [cost:-0.65361==>-0.71383 ; 39 patches optimized, 25 skipped]
lev=4 patch=77x87x75 [clock= 38m 56s 671ms]........... done [cost:-0.71383==>-0.77934 ; 80 patches optimized, 45 skipped]
lev=5 patch=57x65x57 [clock= 48m 38s 759ms]................ done [cost:-0.77934==>-0.83808 ; 160 patches optimized, 92 skipped]
++ ========== total number of parameters 'optimized' = 7497
++ Output dataset ./junk.SSwarper.JLjQnJRzs5c_TAL5_AWARP.nii
++ Output dataset ./junk.SSwarper.JLjQnJRzs5c_TAL5.nii
++ Output dataset ./junk.SSwarper.JLjQnJRzs5c_TAL5_WARP.nii
++ Inverting warp *******............:..
++ Output dataset ./junk.SSwarper.JLjQnJRzs5c_TAL5_WARPINV.nii
++ ===== clock time = 1h 2m 1s 154ms
++ no -frac option: defaulting to -union
++ processing 1 input datasets...
++ padding all datasets by 1 (for dilations)
++ frac 0 over 1 volumes gives min count 0
++ voxel limits: 0 clipped, 2000189 survived, 6529832 were zero
++ writing result junk.SSwarper.JLjQnJRzs5c_MASK.nii...
++ Output dataset ./junk.SSwarper.JLjQnJRzs5c_MASK.nii
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./junk.SSwarper.JLjQnJRzs5c_TAL5mm.nii
++ 3dNwarpApply: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Warped
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as anatS.11987.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:anatS.11987.nii is 0.142653 degrees from plumb.
++ -master dataset is 'anatS.11987.nii'
** AFNI converts NIFTI_datatype=2 (UINT8) in file junk.SSwarper.JLjQnJRzs5c_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 'junk.SSwarper.JLjQnJRzs5c_TAL5mm.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./junk.SSwarper.JLjQnJRzs5c_TAL5ww.nii
++ total Elapsed time = 16.1 sec
++ 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.JLjQnJRzs5c_MASK.nii...
++ Output dataset ./junk.SSwarper.JLjQnJRzs5c_MASK.nii
++ 3dNwarpApply: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Warped
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as anatS.11987.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:anatS.11987.nii is 0.142653 degrees from plumb.
++ -master dataset is 'anatS.11987.nii'
++ opened source dataset 'junk.SSwarper.JLjQnJRzs5c_MASK.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./junk.SSwarper.JLjQnJRzs5c_MASKO.nii
++ total Elapsed time = 12.9 sec
++ 3dcalc: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: dataset 'b'=junk.SSwarper.JLjQnJRzs5c_TAL5ww.nii has an obliquity difference of 0.142653 degrees with anatS.11987.nii
*+ WARNING: dataset 'c'=junk.SSwarper.JLjQnJRzs5c_MASKO.nii has an obliquity difference of 0.142653 degrees with anatS.11987.nii
++ Output dataset ./anatSS.11987.nii
++ 3dAllineate: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the Registrator
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as anatSS.11987.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:anatSS.11987.nii is 0.142653 degrees from plumb.
** AFNI converts NIFTI_datatype=2 (UINT8) in file junk.SSwarper.JLjQnJRzs5c_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: ./anatSS.11987.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 ./junk.SSwarper.JLjQnJRzs5c_AffSS.nii
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 4.7
++ ###########################################################
++ OpenMP thread count = 8
++ 3dQwarp: AFNI version=AFNI_18.1.09 (Apr 30 2018) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=24 xtop=23 ybot=18 ytop=27 zbot=24 ztop=18 voxels
++ Weightizing the base image
++ +++++++++++ Begin warp optimization: base=/home/bmiadmin/abin/MNI152_2009_template.nii.gz source=./junk.SSwarper.JLjQnJRzs5c_AffSS.nii
++ AFNI warpomatic: 240 x 274 x 235 volume ; autobbox = 43..197 38..228 25..188 [clock= 4s 502ms]
lev=3 patch=101x117x99 [clock= 5s 835ms][first cost=-1.60012] ..... done [cost:-1.60012==>-1.70164 ; 16 patches optimized, 11 skipped]
lev=4 patch=77x87x75 [clock= 3m 44s 613ms][first cost=-1.49978] .... done [cost:-1.70164==>-1.54957 ; 37 patches optimized, 27 skipped]
lev=5 patch=57x65x57 [clock= 8m 34s 153ms][first cost=-1.36680] .......:[cost=-1.42939]:.......... done [cost:-1.54957==>-1.43467 ; 241 patches optimized, 191 skipped]
lev=6 patch=43x49x43 [clock= 27m 34s 82ms][first cost=-1.28611] ...........:[cost=-1.34538]:...... done [cost:-1.43467==>-1.36036 ; 502 patches optimized, 394 skipped]
lev=7 patch=33x37x31 [clock= 55m 56s 639ms][first cost=-1.25315] ............................:[cost=-1.30743]:............... done [cost:-1.36036==>-1.29359 ; 1261 patches optimized, 1159 skipped]
lev=8 patch=25x27x23 [clock= 1h 55m 43s 500ms][first cost=-1.23734] .................................:[cost=-1.29184]:............................. done [cost:-1.29359==>-1.23711 ; 3047 patches optimized, 2803 skipped]
lev=9 patch=19x21x17 [clock= 4h 56m 14s 36ms][first cost=-1.24843] .......................... done [cost:-1.23711==>-1.30319 ; 3425 patches optimized, 3358 skipped]
lev=10 patch=13x15x13 [clock= 9h 4m 17s 462ms][first cost=-1.26157] ............................................................................................ done [cost:-1.30319==>-1.22053 ; 9329 patches optimized, 9625 skipped]
lev=11 patch=11x11x11 [clock= 15h 21m 58s 97ms][first cost=-1.26638] .................................