Great, thank you! I updated the AFNI binaries and used the updated script (pasted below). Out of curiosity, how long does the script take to run? I have been processing this script for nearly 18 hours....

Thank you,
Tamara

Code

@SSwarper \
-input 11987.anat+orig \
-base MNI152_2009_template_SSW.nii.gz \
-subid 11987

Terminal output:

-------- 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 \
? -input 11987.anat+orig \
? -base MNI152_2009_template_SSW.nii.gz \
? -subid 11987
SUBJECTS_DIR= /home/bmiadmin/subjects
++ Starting: @SSwarper.
++ OMP_NUM_THREADS is: not set by user,
so probably just using one CPU :(

++ Based on input, the output directory will be:
.

++ 3dUnifize: AFNI version=AFNI_18.2.15 (Aug 28 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................UWGm
++ Output dataset ./anatU.11987.nii
++ ===== Elapsed = 28.8 sec
++ Notice SUMA_BrainWrap_ParseInput (SUMA_3dSkullStrip.c:1219 @13:17:37):
Setting fill_hole to 10
++ Notice 3dSkullStrip (SUMA_3dSkullStrip.c:1529 @13:17:37):
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 236
++mri_brainormalize: bot clip below slice 66
++mri_brainormalize: Rescaling.
++mri_brainormalize: Eroding, clustering ...
+ Eroded 299768 voxels
+ Restored 281809 eroded voxels
+ Clustering voxels ...
+ Largest cluster has 3614900 voxels
+ Clustering voxels ...
+ Largest cluster has 2479512 voxels
++mri_brainormalize: Clipping extreme values.
+ scaling by fac=0.052426
3dSkullStrip: -spatnorm: Expecting 6195700 voxels in in_vol dset (167 212 175)
3dSkullStrip: Edge threshold set to 47.317593. (minimum acceptable was 19.238853)
(92.000000 percentile =47.317593, 99.999001 percentile = 192.388535)
3dSkullStrip: Prepping volume...
SUMA_LoadPrepInVol: Volume 3693983.000000, radius 95.896378
3dSkullStrip: Beginning brain extraction...
3dSkullStrip: Have surface, OK for 1st entry.
3dSkullStrip: Stretching to avoid ventricles.
SO->Center is [1.041406 15.081905 -11.377347]
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: 3140 troubled nodes, going for more...
SUMA_StretchToFitLeCerveau:
In stage 1
SUMA_StretchToFitLeCerveau:
Stage1: pastarea = 83820.069912
SUMA_StretchToFitLeCerveau:
Stage1: MaxExp = 0.706510, 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: 0.078344 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: 0.083621 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: 0.021870 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: 0.009638 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 = 0x2b14cf8) (osnd = 0x3f435b8)...
3dSkullStrip: Coercing...
3dSkullStrip: Writing masked volume ...
3dSkullStrip: Applying a bit of erosion and dilatation
++ OpenMP thread count = 8
++ 3dQwarp: AFNI version=AFNI_18.2.15 (Aug 28 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_SSW.nii.gz[1] -source ./anatU.11987.nii -prefix AFN_8Z6_wZTM8jgi_pO6dkI7Yw.nii -1Dmatrix_save AFN_8Z6_wZTM8jgi_pO6dkI7Yw -cmass -final wsinc5 -float -master BASE -twobest 7 -zclip -fineblur 4.44

++ ###########################################################
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 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_SSW.nii.gz
++ Loading datasets
++ 6526400 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= -1.8432 y-shift=-20.4069 z-shift= 5.4863
z-angle= 1.2094 x-angle= 9.3827 y-angle= 3.0211
x-scale= 0.9033 y-scale= 0.9879 z-scale= 0.8788
y/x-shear= 0.0150 z/x-shear= -0.0178 z/y-shear= -0.0888
++ Output dataset ./AFN_8Z6_wZTM8jgi_pO6dkI7Yw.nii
++ Wrote -1Dmatrix_save AFN_8Z6_wZTM8jgi_pO6dkI7Yw.aff12.1D
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 604.4
++ ###########################################################
++ # Please check results visually for alignment quality #
++ ###########################################################

++ 3dQwarp: replacing source dataset with 3dAllineate result ./junk.SSwarper.aGKqAz94Dmb_TAL5_Allin.nii
+ 3dAllineate output files have been renamed
# mat44 3dAllineate matrix:
0.901673 0.026798 -0.046970 -1.843160
-0.007067 0.974836 0.160347 -20.406900
0.035061 -0.229067 0.852391 5.486270
++ 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_SSW.nii.gz source=./junk.SSwarper.aGKqAz94Dmb_TAL5_Allin.nii
++ AFNI warpomatic: 240 x 274 x 235 volume ; autobbox = 30..209 31..243 30..204 [clock= 10m 6s 691ms]
lev=0 8..231 5..269 9..225: [first cost=-0.44256] .. done [cost:-0.44256==>-0.55219]
lev=1 patch=181x207x177 [clock= 12m 20s 641ms]........ done [cost:-0.55219==>-0.58722 ; 8 patches optimized, 0 skipped]
lev=2 patch=135x155x133 [clock= 14m 58s 350ms]..................... done [cost:-0.58722==>-0.65454 ; 21 patches optimized, 6 skipped]
lev=3 patch=101x117x99 [clock= 18m 46s 894ms]............. done [cost:-0.65454==>-0.71108 ; 39 patches optimized, 25 skipped]
lev=4 patch=77x87x75 [clock= 26m 24s 319ms]............ done [cost:-0.71108==>-0.77957 ; 80 patches optimized, 45 skipped]
lev=5 patch=57x65x57 [clock= 35m 0s 294ms]........... done [cost:-0.77957==>-0.84085 ; 160 patches optimized, 92 skipped]
++ ========== total number of parameters 'optimized' = 7497
++ Output dataset ./junk.SSwarper.aGKqAz94Dmb_TAL5_AWARP.nii
++ Output dataset ./junk.SSwarper.aGKqAz94Dmb_TAL5.nii
++ Output dataset ./junk.SSwarper.aGKqAz94Dmb_TAL5_WARP.nii
++ Inverting warp ********............:..
++ Output dataset ./junk.SSwarper.aGKqAz94Dmb_TAL5_WARPINV.nii
++ ===== clock time = 45m 39s 574ms
++ 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.aGKqAz94Dmb_MASK.nii...
++ Output dataset ./junk.SSwarper.aGKqAz94Dmb_MASK.nii
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ././junk.SSwarper.aGKqAz94Dmb_TAL5mm.nii
++ 3dNwarpApply: AFNI version=AFNI_18.2.15 (Aug 28 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.aGKqAz94Dmb_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.aGKqAz94Dmb_TAL5mm.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./junk.SSwarper.aGKqAz94Dmb_TAL5ww.nii
++ total Elapsed time = 17.6 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.aGKqAz94Dmb_MASK.nii...
++ Output dataset ./junk.SSwarper.aGKqAz94Dmb_MASK.nii
++ 3dNwarpApply: AFNI version=AFNI_18.2.15 (Aug 28 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.aGKqAz94Dmb_MASK.nii'
++ Processing -nwarp
++ Warping:.Z
++ Output dataset ./junk.SSwarper.aGKqAz94Dmb_MASKO.nii
++ total Elapsed time = 13.6 sec
++ 3dcalc: AFNI version=AFNI_18.2.15 (Aug 28 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: dataset 'b'=./junk.SSwarper.aGKqAz94Dmb_TAL5ww.nii has an obliquity difference of 0.142653 degrees with ./anatS.11987.nii
*+ WARNING: dataset 'c'=./junk.SSwarper.aGKqAz94Dmb_MASKO.nii has an obliquity difference of 0.142653 degrees with ./anatS.11987.nii
++ Output dataset ././anatSS.11987.nii
++ 3dAllineate: AFNI version=AFNI_18.2.15 (Aug 28 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.aGKqAz94Dmb_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.aGKqAz94Dmb_AffSS.nii
++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 4.8
++ ###########################################################
++ OpenMP thread count = 8
++ 3dQwarp: AFNI version=AFNI_18.2.15 (Aug 28 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_SSW.nii.gz source=./junk.SSwarper.aGKqAz94Dmb_AffSS.nii
++ AFNI warpomatic: 240 x 274 x 235 volume ; autobbox = 43..197 38..228 25..188 [clock= 4s 682ms]
lev=1 patch=181x207x177 [clock= 6s 586ms][first cost=-1.88256] . done [cost:-1.88256==>-1.95521 ; 1 patches optimized, 8 skipped]
lev=2 patch=135x155x133 [clock= 27s 11ms][first cost=-1.80056] . done [cost:-1.95521==>-1.81904 ; 1 patches optimized, 7 skipped]
lev=3 patch=101x117x99 [clock= 42s 15ms][first cost=-1.45511] ...... done [cost:-1.81904==>-1.64769 ; 16 patches optimized, 11 skipped]
lev=4 patch=77x87x75 [clock= 4m 6s 394ms][first cost=-1.43211] ........... done [cost:-1.64769==>-1.53197 ; 37 patches optimized, 27 skipped]
lev=5 patch=57x65x57 [clock= 8m 31s 129ms][first cost=-1.34005] ......:[cost=-1.43214]:............ done [cost:-1.53197==>-1.45969 ; 241 patches optimized, 191 skipped]
lev=6 patch=43x49x43 [clock= 28m 2s 265ms][first cost=-1.29349] ........:[cost=-1.34350]:............ done [cost:-1.45969==>-1.35091 ; 502 patches optimized, 394 skipped]
lev=7 patch=33x37x31 [clock= 57m 46s 316ms][first cost=-1.24965] ..........:[cost=-1.30697]:....................... done [cost:-1.35091==>-1.27698 ; 1261 patches optimized, 1159 skipped]
lev=8 patch=25x27x23 [clock= 1h 56m 28s 428ms][first cost=-1.23410] ....................:[cost=-1.29141]:......................... done [cost:-1.27698==>-1.22973 ; 3047 patches optimized, 2803 skipped]
lev=9 patch=19x21x17 [clock= 4h 2m 28s 66ms][first cost=-1.24622] ........................................ done [cost:-1.22973==>-1.30171 ; 3425 patches optimized, 3358 skipped]
lev=10 patch=13x15x13 [clock= 6h 17m 59s 942ms][first cost=-1.26016] ............................................................................................ done [cost:-1.30171==>-1.20685 ; 9329 patches optimized, 9625 skipped]
lev=11 patch=11x11x11 [clock= 12h 19m 35s 471ms][first cost=-1.26158] ....................................................................