options for -epi_base on align_epi_anat.py

wgraves · March 8, 2023, 9:05pm

Hello AFNI experts,

Apologies if this is a repeat question. I did do a search of the message board and found no relevant results.

When using align_epi_anat.py, I tried specifying for -epi_base the option, mean. Here’s my actual command:

align_epi_anat.py -anat MPRAGE_sag_CM+orig -epi sw3_CM+orig -anat2epi -giant_move -cost lpc+ -epi_base mean -child_epi sw1_CM+orig sw2_CM+orig sw4_CM+orig sw5_CM+orig sw6_CM+orig -tshift_opts “-ignore $tignore” -output_dir $datadir/$subj/func -save_vr -suffix _al -overwrite

And here’s the error it returned:
** ERROR: selector syntax error 5 ‘mean]’
** ERROR: bad sub-brick selector [mean]
** FATAL ERROR: Couldn’t open -base dataset ./sw3_CM+orig[mean]

Am I just misunderstanding this option? I assumed it would calculate the mean when specified. Is that not what it does, or am I just using it wrong?

Best,
Will

ptaylor · March 8, 2023, 11:08pm

Hi, Will-

Hmm, weird. I ran this similar command (just didn’t have followers and ts_shifts, but those should not affect this) and did not get the same error:


align_epi_anat.py                                                            \
    -anat         FT_anat+orig.HEAD                                          \
    -epi          pb00.FT.r01.tcat+orig.HEAD                                 \
    -anat2epi                                                                \
    -giant_move                                                              \
    -cost         lpc+                                                       \
    -epi_base     mean                                                       \
    -output_dir   ./odir                                                     \
    -save_vr                                                                 \
    -suffix       _al                                                        \
    -overwrite

And your understanding of what should be happening there is correct, yes.

Ummm, I am not sure why it would be different for you. Having a non-numeric argument after “-epi_base …” should trigger a 3dTstat command, so it shouldn’t be trying to use that argument as a subbrick selector.

Just out of curiosity, what is your “afni -ver”? Also, is there more text output by the command before that failure, in case that might provide any clues? And perhaps could you run it with “-verb 5” as an extra option, and copy+paste the output text here?

thanks,
pt

wgraves · March 9, 2023, 2:24am

Sure thing, Paul. Thanks for getting back to me. Here’s the output of “afni -ver”:

Precompiled binary linux_ubuntu_16_64: Jan 24 2023 (Version AFNI_23.0.02 ‘Commodus’)

And when I run this command:
align_epi_anat.py -verb 5 -anat MPRAGE_sag_CM+orig -epi sw3_CM+orig -anat2epi -ginormous_move -cost lpc+ -epi_base mean -child_epi sw1_CM+orig sw2_CM+orig sw4_CM+orig sw5_CM+orig sw6_CM+orig -tshift_opts “-ignore $tignore” -output_dir $datadir/$subj/func -save_vr -suffix _al -overwrite

Here’s the full output this time (it gets quite far before erroring out):

#++ align_epi_anat version: 1.63
------ found options ------ : align_epi_anat.py
valid_opts: OptionList: init_opts (len 97)
opt 00: -epi
opt 01: -dset2
opt 02: -anat
opt 03: -dset1
opt 04: -keep_rm_files
opt 05: -prep_only
opt 06: -help
opt 07: -limited_help
opt 08: -option_help
opt 09: -version
opt 10: -ver
opt 11: -verb
opt 12: -save_script
opt 13: -align_centers
opt 14: -anat_has_skull
opt 15: -epi_strip
opt 16: -dset1_strip
opt 17: -dset2_strip
opt 18: -volreg_method
opt 19: -ex_mode
opt 20: -overwrite
opt 21: -big_move
opt 22: -giant_move
opt 23: -ginormous_move
opt 24: -supersize
opt 25: -rigid_body
opt 26: -rigid_equiv
opt 27: -partial_coverage
opt 28: -partial_axial
opt 29: -partial_coronal
opt 30: -partial_sagittal
opt 31: -AddEdge
opt 32: -Allineate_opts
opt 33: -perc
opt 34: -suffix
opt 35: -cost
opt 36: -multi_cost
opt 37: -check_cost
opt 38: -epi2anat
opt 39: -anat2epi
opt 40: -dset2to1
opt 41: -dset1to2
opt 42: -epi_base
opt 43: -dset2_base
opt 44: -volreg_base
opt 45: -volreg
opt 46: -volreg_opts
opt 47: -tshift
opt 48: -tshift_opts
opt 49: -deoblique
opt 50: -deoblique_opts
opt 51: -resample
opt 52: -prep_off
opt 53: -cmass
opt 54: -tlrc_apar
opt 55: -tlrc_epar
opt 56: -auto_tlrc
opt 57: -child_epi
opt 58: -child_dset2
opt 59: -child_anat
opt 60: -child_dset1
opt 61: -master_epi
opt 62: -master_dset2
opt 63: -master_tlrc
opt 64: -master_anat
opt 65: -master_dset1
opt 66: -master_anat_dxyz
opt 67: -master_dset1_dxyz
opt 68: -master_epi_dxyz
opt 69: -master_dset2_dxyz
opt 70: -master_tlrc_dxyz
opt 71: -pre_matrix
opt 72: -post_matrix
opt 73: -skullstrip_opts
opt 74: -dset1strip_opts
opt 75: -epistrip_opts
opt 76: -dset2strip_opts
opt 77: -feature_size
opt 78: -rat_align
opt 79: -output_dir
opt 80: -edge
opt 81: -edge_erodelevel
opt 82: -check_flip
opt 83: -flip_giant
opt 84: -save_Al_in
opt 85: -save_vr
opt 86: -save_tsh
opt 87: -save_skullstrip
opt 88: -save_orig_skullstrip
opt 89: -save_epi_ns
opt 90: -save_rep
opt 91: -save_resample
opt 92: -save_all
opt 93: -pow_mask
opt 94: -bin_mask
opt 95: -box_mask
opt 96: -mask
user_opts: OptionList: read_options (len 23)
opt 00: -verb args found = 1
opt 01: -anat args found = 1
opt 02: -epi args found = 1
opt 03: -anat2epi
opt 04: -ginormous_move
opt 05: -cost args found = 1
opt 06: -epi_base args found = 1
opt 07: -child_epi args found = 5
opt 08: -tshift_opts args found = 1
opt 09: -output_dir args found = 1
opt 10: -save_vr
opt 11: -suffix args found = 1
opt 12: -overwrite
opt 13: -align_centers
opt 14: -volreg_method
opt 15: -ex_mode
opt 16: -Allineate_opts
opt 17: -perc
opt 18: -volreg_opts
opt 19: -pow_mask
opt 20: -bin_mask
opt 21: -box_mask
opt 22: -mask
#++ -child_epi or child_dset2 option given
#++ Child epis / dset2 will be processed although not aligning
epi to anat datasets with -epi2anat / -dset2to1 because a
save preprocessing option such as -save_vr is selected
#++ Found child epi/dset2 /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw1_CM+orig

#++ Found child epi/dset2 /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw2_CM+orig

#++ Found child epi/dset2 /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw4_CM+orig

#++ Found child epi/dset2 /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw5_CM+orig

#++ Found child epi/dset2 /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw6_CM+orig

#Script is running (command trimmed):
3dAttribute DELTA ./sw3_CM+orig
#Script is running (command trimmed):
3dAttribute DELTA ./sw3_CM+orig
#Script is running (command trimmed):
3dAttribute DELTA ./MPRAGE_sag_CM+orig
#++ Multi-cost is lpc+

User has selected a new output directory /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/

#Script is running (command trimmed):
mkdir ./
mkdir: cannot create directory ‘./’: File exists
cd /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/
#++ Removing all the temporary files
#Script is running (command trimmed):
\rm -f ./__tt_sw3_CM*
#Script is running (command trimmed):
\rm -f ./__tt_MPRAGE_sag_CM*
#Script is running (command trimmed):
3dcopy ./MPRAGE_sag_CM+orig ./__tt_MPRAGE_sag_CM+orig
++ 3dcopy: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
#++ Removing skull from anat data
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_MPRAGE_sag_CM+orig -prefix ./__tt_MPRAGE_sag_CM_ns
#Script is running (command trimmed):
3dinfo ./__tt_MPRAGE_sag_CM_ns+orig | \grep ‘Data Axes Tilt:’|\grep ‘Oblique’
#++ Dataset /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/__tt_MPRAGE_sag_CM_ns+orig is not oblique
#Script is running (command trimmed):
3dinfo ./sw3_CM+orig | \grep ‘Data Axes Tilt:’|\grep ‘Oblique’
#++ Dataset /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw3_CM+orig is not oblique
#Script is running (command trimmed):
3dAttribute DELTA ./__tt_MPRAGE_sag_CM_ns+orig
#++ Spacing for anat to oblique epi alignment is 1.000000
#Script is running (command trimmed):
3dcopy ./__tt_MPRAGE_sag_CM_ns+orig ./__tt_MPRAGE_sag_CM_ns_ob; @Align_Centers -base ./sw3_CM+orig -dset ./__tt_MPRAGE_sag_CM_ns_ob+orig -no_cp
++ 3dcopy: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ 3drefit: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./__tt_MPRAGE_sag_CM_ns_ob+orig

deoblique
++ 3drefit processed 1 datasets
#Script is running (command trimmed):
cat_matvec ./__tt_MPRAGE_sag_CM_ns_ob_shft.1D -I > ./__tt_MPRAGE_sag_CM_ns_shft_I.1D
#Script is running (command trimmed):
3dAttribute TAXIS_OFFSETS ./sw3_CM+orig
#++ Correcting for slice timing
#Script is running (command trimmed):
3dTshift -prefix ./__tt_sw3_CM_tsh -ignore 4 ./sw3_CM+orig
++ 3dTshift: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ updating time offset to 0.971428
#Script is running (command trimmed):
rm ./sw3_CM_tsh_vr+orig.HEAD
#Script is running (command trimmed):
rm ./sw3_CM_tsh_vr+orig.BRIK.gz
#++ Volume registration for epi data
#Script is running (command trimmed):
3dTstat -mean -prefix ./sw3_CM_tsh_vr_ts_tempalpha ./__tt_sw3_CM_tsh+orig
++ 3dTstat: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ Authored by: KR Hammett & RW Cox
#Script is running (command trimmed):
3dvolreg -prefix ./sw3_CM_tsh_vr_vr_tempalpha -base ./sw3_CM_tsh_vr_ts_tempalpha+orig’[0]’ -cubic ./__tt_sw3_CM_tsh+orig
++ 3dvolreg: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ Authored by: RW Cox
++ Max displacement in automask = 4.49 (mm) at sub-brick 27
++ Max delta displ in automask = 1.72 (mm) at sub-brick 48
#Script is running (command trimmed):
3dTstat -mean -prefix ./sw3_CM_tsh_vr_vrt ./sw3_CM_tsh_vr_vr_tempalpha+orig
++ 3dTstat: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ Authored by: KR Hammett & RW Cox
#Script is running (command trimmed):
3dvolreg -1Dfile ./sw3_CM_tsh_vr_motion.1D -1Dmatrix_save ./sw3_CM_tsh_vr_mat.aff12.1D -prefix ./sw3_CM_tsh_vr -base ./sw3_CM_tsh_vr_vrt+orig’[0]’ -cubic ./__tt_sw3_CM_tsh+orig
++ 3dvolreg: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ Authored by: RW Cox
++ Max displacement in automask = 4.55 (mm) at sub-brick 27
++ Max delta displ in automask = 1.73 (mm) at sub-brick 48
** Warning: overwriting file ./sw3_CM_tsh_vr_motion.1D
#++ Creating representative epi sub-brick
#Script is running (command trimmed):
3dTstat -mean -prefix ./__tt_sw3_CM_tsh_vr_ts ./sw3_CM_tsh_vr+orig
++ 3dTstat: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ Authored by: KR Hammett & RW Cox
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_sw3_CM_tsh_vr_ts+orig -prefix ./__tt_sw3_CM_tsh_vr_ts_ns
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 ./__tt_sw3_CM_tsh_vr_ts_ns+orig
#++ Applying threshold of 893.349976 on /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/__tt_sw3_CM_tsh_vr_ts_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix ./__tt_sw3_CM_tsh_vr_ts_ns_wt -a ./__tt_sw3_CM_tsh_vr_ts_ns+orig -expr ‘min(1,(a/893.349976))’
++ 3dcalc: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ Authored by: A cast of thousands
#++ Aligning anat data to epi data
#Script is running (command trimmed):
3dAllineate -lpc+ -wtprefix ./__tt_MPRAGE_sag_CM_ns_ob_al_wtal -weight ./__tt_sw3_CM_tsh_vr_ts_ns_wt+orig -source ./__tt_MPRAGE_sag_CM_ns_ob+orig -prefix ./__tt_MPRAGE_sag_CM_ns_ob_temp_al -base ./__tt_sw3_CM_tsh_vr_ts_ns+orig -cmass -1Dmatrix_save ./MPRAGE_sag_CM_al_e2a_only_mat.aff12.1D -master BASE -mast_dxyz 1.000000 -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2
++ 3dAllineate: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ Authored by: Zhark the Registrator
++ Option ‘-cmass’ enables center-of-mass code = 7 = +xyz
++ Source dataset: ./__tt_MPRAGE_sag_CM_ns_ob+orig.HEAD
++ Base dataset: ./__tt_sw3_CM_tsh_vr_ts_ns+orig.HEAD
++ Loading datasets into memory
++ 1641787 voxels in -source_automask+2
++ largeness ==> set -twobest 29
++ Zero-pad: ybot=5 ytop=6
++ Zero-pad: zbot=8 ztop=8
++ 54513 voxels [22.3%] in weight mask
++ Number of points for matching = 54513
++ NOTE: base and source coordinate systems have different handedness

  Orientations: base=Right handed (RAI); 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 = ‘TOHD(15.6923)’
++ lpc+ parameters: hel=0.40 mi=0.20 nmi=0.20 crA=0.40 ov=0.40
++ base center of mass = 32.232 39.227 26.379 (index)

source center of mass = 151.833 106.672 88.684 (index)
source-target CM = -1.046 16.024 16.690 (xyz)
estimated center of mass shifts = -1.046 16.024 16.690
++ shift param auto-range: -62.7…60.6 -56.4…88.4 -31.5…64.8
Range param#4 [z-angle] = -6.000000 … 6.000000 center = 0.000000
Range param#5 [x-angle] = -6.000000 … 6.000000 center = 0.000000
Range param#6 [y-angle] = -6.000000 … 6.000000 center = 0.000000
Range param#1 [x-shift] = -11.046204 … 8.953796 center = -1.046204
Range param#2 [y-shift] = 6.024437 … 26.024437 center = 16.024437
Range param#3 [z-shift] = 6.690224 … 26.690224 center = 16.690224
Range param#4 [z-angle] = -45.000000 … 45.000000 center = 0.000000
Range param#5 [x-angle] = -45.000000 … 45.000000 center = 0.000000
Range param#6 [y-angle] = -45.000000 … 45.000000 center = 0.000000
Range param#1 [x-shift] = -41.046204 … 38.953796 center = -1.046204
Range param#2 [y-shift] = -23.975563 … 56.024437 center = 16.024437
Range param#3 [z-shift] = -23.309776 … 56.690224 center = 16.690224
12 free parameters
++ Normalized (unitless) convergence radius = 0.0000094
++ Final parameter search ranges:
```
  x-shift =  -41.046 ..   38.954
```
```
  y-shift =  -23.976 ..   56.024
```
```
  z-shift =  -23.310 ..   56.690
```
```
  z-angle =  -45.000 ..   45.000
```
```
  x-angle =  -45.000 ..   45.000
```
```
  y-angle =  -45.000 ..   45.000
```
```
  x-scale =    0.711 ..    1.406
```
```
  y-scale =    0.711 ..    1.406
```
```
  z-scale =    0.711 ..    1.406
```
```
y/x-shear =   -0.111 ..    0.111
```
```
z/x-shear =   -0.111 ..    0.111
```
```
z/y-shear =   -0.111 ..    0.111
```

++ changing output grid spacing to 1.0000 mm
++ OpenMP thread count = 15
++ ======= Allineation of 1 sub-bricks using Local Pearson Signed + Others =======

source mask has 1641787 [out of 11534336] voxels
base mask has 66681 [out of 244800] voxels
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]
++ *** Coarse pass begins ***
- Enter alignment setup routine
- copying base image
- copying source image
- Smoothing base; radius=3.05
- Smoothing source; radius=3.05
!source mask fill: ubot=70 usiz=180
- copying weight image
- using 54513 points from base image [use_all=2]
- Exit alignment setup routine
- Search for coarse starting parameters
- histogram: source clip 106.24 … 435.34; base clip 255.532 … 920.773
- versus source range 1.32789 … 415.465; base range 0 … 1183.25
46870 total points stored in 93 ‘TOHD(15.9854)’ bloks (0 duplicates)
- number of free params = 6
- Test (64+191)*64 params [top5=*o±.]:#oooo.-+.-.o-$ + - best 88 costs found:
  o= 0 v= 0.509267: -1.05 16.02 16.69 0.00 0.00 0.00 [grid]
  o= 1 v= 0.729684: -7.71 9.36 23.36 7.50 7.50 -7.50 [grid]
  o= 2 v= 0.743124: -7.71 9.36 23.36 7.50 7.50 7.50 [grid]
  o= 3 v= 0.765238: 5.62 9.36 23.36 -7.50 7.50 -7.50 [grid]
  o= 4 v= 0.776518: 5.62 9.36 23.36 -7.50 7.50 7.50 [grid]
  o= 5 v= 0.785511: -7.71 9.36 23.36 7.50 -7.50 7.50 [grid]
  o= 6 v= 0.804293: -7.71 9.36 23.36 7.50 -7.50 -7.50 [grid]
  o= 7 v= 0.817091: -7.71 9.36 23.36 -7.50 7.50 -7.50 [grid]
  o= 8 v= 0.823613: 5.62 9.36 23.36 -7.50 -7.50 -7.50 [grid]
  o= 9 v= 0.826522: 5.62 9.36 23.36 -7.50 -7.50 7.50 [grid]
  o=10 v= 0.836143: -7.71 9.36 23.36 -7.50 -7.50 7.50 [grid]
  o=11 v= 0.836580: 5.62 9.36 23.36 7.50 7.50 7.50 [grid]
  o=12 v= 0.836960: -7.71 9.36 23.36 30.00 7.50 -7.50 [grid]
  o=13 v= 0.844207: -7.71 9.36 23.36 -7.50 7.50 7.50 [grid]
  o=14 v= 0.848563: -7.71 22.69 23.36 -7.50 -7.50 7.50 [grid]
  o=15 v= 0.850290: 5.62 9.36 23.36 7.50 -7.50 -7.50 [grid]
  o=16 v= 0.850458: 5.62 9.36 23.36 7.50 7.50 -7.50 [grid]
  o=17 v= 0.853545: 5.62 22.69 23.36 7.50 -7.50 -7.50 [grid]
  o=18 v= 0.862039: -7.71 22.69 23.36 -7.50 -7.50 -7.50 [grid]
  o=19 v= 0.862838: -7.71 9.36 23.36 30.00 7.50 7.50 [grid]
  o=20 v= 0.862913: 5.62 22.69 23.36 7.50 -7.50 7.50 [grid]
  o=21 v= 0.866326: -7.71 9.36 23.36 -7.50 -7.50 -7.50 [grid]
  o=22 v= 0.873110: 5.62 9.36 23.36 7.50 -7.50 7.50 [grid]
  o=23 v= 0.878079: -7.71 22.69 23.36 -7.50 7.50 -7.50 [grid]
  o=24 v= 0.882023: -7.71 22.69 10.02 -7.50 7.50 -7.50 [grid]
  o=25 v= 0.884183: -7.71 22.69 10.02 -7.50 7.50 7.50 [grid]
  o=26 v= 0.886567: -7.71 22.69 23.36 -7.50 7.50 7.50 [grid]
  o=27 v= 0.892038: -7.71 22.69 23.36 7.50 7.50 7.50 [grid]
  o=28 v= 0.896387: 5.62 22.69 10.02 7.50 7.50 7.50 [grid]
  o=29 v= 0.899968: 5.62 22.69 23.36 7.50 7.50 7.50 [grid]
  o=30 v= 0.900960: 5.62 22.69 23.36 7.50 7.50 -7.50 [grid]
  o=31 v= 0.901282: -7.71 22.69 23.36 7.50 7.50 -7.50 [grid]
  o=32 v= 0.903887: 5.62 22.69 10.02 7.50 7.50 -7.50 [grid]
  o=33 v= 0.907423: -7.71 9.36 23.36 7.50 7.50 30.00 [grid]
  o=34 v= 0.908694: 5.62 9.36 23.36 -30.00 7.50 -7.50 [grid]
  o=35 v= 0.911926: 5.62 22.69 23.36 -7.50 7.50 -7.50 [grid]
  o=36 v= 0.919621: 5.62 9.36 23.36 -30.00 7.50 7.50 [grid]
  o=37 v= 0.926626: -7.71 22.69 23.36 7.50 -7.50 7.50 [grid]
  o=38 v= 0.932293: -7.71 9.36 23.36 30.00 -7.50 -7.50 [grid]
  o=39 v= 0.937786: -7.71 22.69 23.36 7.50 -7.50 -7.50 [grid]
  o=40 v= 0.938804: 5.62 22.69 23.36 -7.50 7.50 7.50 [grid]
  o=41 v= 0.938916: 5.62 22.69 23.36 -7.50 -7.50 7.50 [grid]
  o=42 v= 0.938936: 5.62 9.36 23.36 -7.50 7.50 -30.00 [grid]
  o=43 v= 0.947469: 3.03 9.80 24.49 -4.32 22.85 -18.95 [rand]
  o=44 v= 0.951429: -7.71 9.36 10.02 7.50 -7.50 -7.50 [grid]
  o=45 v= 0.952123: 5.62 22.69 23.36 -7.50 -7.50 -7.50 [grid]
  o=46 v= 0.958263: 3.03 9.80 24.49 4.32 22.85 -18.95 [rand]
  o=47 v= 0.958771: -7.71 9.36 23.36 7.50 7.50 -30.00 [grid]
  o=48 v= 0.962315: -7.71 9.36 10.02 7.50 -7.50 7.50 [grid]
  o=49 v= 0.965963: -7.71 22.69 10.02 7.50 7.50 -7.50 [grid]
  o=50 v= 0.966089: -5.13 9.80 24.49 4.32 22.85 -18.95 [rand]
  o=51 v= 0.968032: -5.13 9.80 24.49 4.32 22.85 18.95 [rand]
  o=52 v= 0.968647: 5.62 9.36 23.36 -7.50 7.50 30.00 [grid]
  o=53 v= 0.975410: -7.71 9.36 23.36 -7.50 7.50 30.00 [grid]
  o=54 v= 0.976117: -7.71 9.36 23.36 30.00 7.50 -30.00 [grid]
  o=55 v= 0.976941: 5.62 9.36 23.36 7.50 7.50 -30.00 [grid]
  o=56 v= 0.978731: -7.71 9.36 23.36 7.50 -7.50 -30.00 [grid]
  o=57 v= 0.979912: 5.62 9.36 23.36 -7.50 -7.50 30.00 [grid]
  o=58 v= 0.979997: 5.62 9.36 10.02 -7.50 -7.50 7.50 [grid]
  o=59 v= 0.980066: 5.62 9.36 10.02 -7.50 -7.50 -7.50 [grid]
  o=60 v= 0.983750: -7.71 9.36 23.36 7.50 -7.50 30.00 [grid]
  o=61 v= 0.990436: 5.62 22.69 10.02 -7.50 7.50 7.50 [grid]
  o=62 v= 0.992120: -7.71 9.36 23.36 30.00 -7.50 -30.00 [grid]
  o=63 v= 0.993324: -5.13 9.80 24.49 -4.32 22.85 18.95 [rand]
  o=64 v= 0.996164: -7.71 9.36 23.36 30.00 -7.50 7.50 [grid]
  o=65 v= 1.003487: 5.62 9.36 23.36 -30.00 -7.50 7.50 [grid]
  o=66 v= 1.006020: -7.71 22.69 10.02 7.50 7.50 7.50 [grid]
  o=67 v= 1.011582: 5.62 22.69 10.02 -7.50 7.50 -7.50 [grid]
  o=68 v= 1.013242: -5.13 9.80 24.49 -4.32 22.85 -18.95 [rand]
  o=69 v= 1.016648: -7.71 9.36 23.36 -7.50 7.50 -30.00 [grid]
  o=70 v= 1.018148: -7.71 9.36 10.02 7.50 7.50 -7.50 [grid]
  o=71 v= 1.020849: -7.71 9.36 23.36 30.00 7.50 30.00 [grid]
  o=72 v= 1.024592: 5.62 9.36 23.36 -7.50 -7.50 -30.00 [grid]
  o=73 v= 1.025507: -7.71 9.36 10.02 7.50 7.50 7.50 [grid]
  o=74 v= 1.027457: 3.03 9.80 24.49 -4.32 22.85 18.95 [rand]
  o=75 v= 1.029387: 5.62 9.36 10.02 7.50 -7.50 -7.50 [grid]
  o=76 v= 1.029459: 5.62 9.36 23.36 7.50 7.50 30.00 [grid]
  o=77 v= 1.034515: -7.71 22.69 23.36 -7.50 7.50 -30.00 [grid]
  o=78 v= 1.034687: -7.71 9.36 23.36 -7.50 -7.50 30.00 [grid]
  o=79 v= 1.035177: 5.62 9.36 10.02 -7.50 7.50 7.50 [grid]
  o=80 v= 1.039029: 5.62 9.36 23.36 30.00 7.50 7.50 [grid]
  o=81 v= 1.040023: -3.45 1.93 26.63 5.34 3.42 -10.89 [rand]
  o=82 v= 1.040747: 5.62 9.36 23.36 7.50 -7.50 -30.00 [grid]
  o=83 v= 1.041866: 5.62 9.36 23.36 -30.00 -7.50 30.00 [grid]
  o=84 v= 1.042048: -3.45 1.93 26.63 5.34 -3.42 -10.89 [rand]
  o=85 v= 1.042886: -7.71 22.69 23.36 -7.50 -7.50 30.00 [grid]
  o=86 v= 1.043111: 5.62 9.36 10.02 7.50 7.50 -7.50 [grid]
  o=87 v= 1.045174: 5.62 9.36 23.36 7.50 -7.50 30.00 [grid]
- A little optimization:*[#16324=0.344329] *[#16332=0.341682] *[#16334=0.341097] *[#16336=0.33636] *[#16337=0.333565] *[#16338=0.327819] *[#16342=0.312009] *[#16346=0.311542] [#16349=0.309422] [#16355=0.308867] .[#16412=0.308258] …[#16598=0.307506] [#16603=0.307343] …[#16975=0.307174] *[#16984=0.306676] …
- costs of the above after a little optimization:
  o= 0 v= 0.308867: -1.30 15.29 19.99 1.13 0.10 0.01 [grid] [f=36]
  o= 1 v= 0.308258: -1.44 15.02 20.15 1.58 0.18 -0.23 [grid] [f=60]
  o= 2 v= 0.308391: -1.49 15.29 20.12 1.34 -0.08 -0.24 [grid] [f=60]
  o= 3 v= 0.308534: -1.66 14.93 20.17 1.62 0.23 -0.17 [grid] [f=65]
  o= 4 v= 0.307343: -1.53 15.04 20.05 1.57 0.14 -0.13 [grid] [f=61]
  o= 5 v= 0.307872: -1.64 14.96 19.87 1.61 -0.07 -0.09 [grid] [f=65]
  o= 6 v= 0.309036: -1.41 15.36 20.15 1.21 -0.17 0.03 [grid] [f=56]
  o= 7 v= 0.308406: -1.46 15.26 20.09 1.37 -0.05 -0.22 [grid] [f=57]
  o= 8 v= 0.308997: -1.39 15.23 20.11 1.32 -0.17 0.13 [grid] [f=60]
  o= 9 v= 0.311387: -1.60 15.44 19.85 1.64 -0.62 -0.14 [grid] [f=69]
  *o=10 v= 0.306676: -1.57 15.01 19.98 1.61 0.08 0.03 [grid] [f=66]
  o=11 v= 0.309691: -1.56 15.30 19.92 1.45 -0.32 -0.14 [grid] [f=55]
  o=12 v= 0.309221: -1.52 15.22 20.16 1.46 -0.09 -0.09 [grid] [f=61]
  o=13 v= 0.310475: -1.37 15.30 19.96 1.33 -0.27 0.13 [grid] [f=66]
  o=14 v= 0.308173: -1.34 15.31 20.16 1.31 0.17 -0.26 [grid] [f=66]
  o=15 v= 0.309485: -1.40 15.41 20.05 1.51 -0.13 -0.33 [grid] [f=57]
  o=16 v= 0.308550: -1.55 15.01 20.21 1.60 0.24 -0.24 [grid] [f=65]
  o=17 v= 0.308370: -1.54 15.12 20.13 1.54 0.12 -0.21 [grid] [f=74]
  o=18 v= 0.309202: -1.61 15.00 19.86 1.64 -0.10 0.12 [grid] [f=77]
  o=19 v= 0.310367: -1.61 15.37 19.91 1.60 -0.46 -0.22 [grid] [f=66]
  o=20 v= 0.308065: -1.43 15.31 20.05 1.35 0.11 -0.17 [grid] [f=62]
  o=21 v= 0.309654: -1.37 15.39 20.06 1.15 -0.05 0.33 [grid] [f=56]
  o=22 v= 0.308656: -1.54 15.02 20.11 1.71 0.17 -0.33 [grid] [f=58]
  o=23 v= 0.311370: -1.22 15.54 20.10 0.86 -0.30 0.10 [grid] [f=64]
  o=24 v= 0.307606: -1.47 15.13 20.00 1.49 0.07 -0.04 [grid] [f=83]
  o=25 v= 0.308402: -1.42 15.28 20.12 1.32 -0.16 -0.20 [grid] [f=70]
  o=26 v= 0.309389: -1.50 15.40 20.11 1.52 -0.14 0.18 [grid] [f=63]
  o=27 v= 0.308283: -1.37 15.37 20.00 1.21 0.08 -0.04 [grid] [f=53]
  o=28 v= 0.311464: -1.31 15.27 20.03 1.30 -0.27 0.40 [grid] [f=83]
  o=29 v= 0.309803: -1.48 15.31 20.14 1.60 0.13 -0.28 [grid] [f=60]
  o=30 v= 0.310167: -1.29 15.43 20.17 1.19 0.01 -0.08 [grid] [f=61]
  o=31 v= 0.308280: -1.53 15.29 20.14 1.38 -0.18 -0.12 [grid] [f=60]
  o=32 v= 0.309065: -1.49 15.36 20.15 1.41 -0.14 -0.16 [grid] [f=73]
  o=33 v= 0.308555: -1.64 15.06 19.85 1.59 -0.01 -0.18 [grid] [f=64]
  o=34 v= 0.307777: -1.54 15.16 20.08 1.57 0.16 -0.08 [grid] [f=76]
  o=35 v= 0.309890: -1.51 15.40 20.02 1.41 -0.01 0.14 [grid] [f=69]
  o=36 v= 0.308566: -1.44 15.33 19.98 1.31 -0.10 -0.40 [grid] [f=70]
  o=37 v= 0.309200: -1.46 15.26 20.15 1.38 -0.24 -0.01 [grid] [f=63]
  o=38 v= 0.308585: -1.42 15.03 19.96 1.54 -0.01 -0.03 [grid] [f=83]
  o=39 v= 0.308119: -1.51 15.30 20.04 1.36 -0.08 -0.28 [grid] [f=61]
  o=40 v= 0.309787: -1.54 15.15 20.06 1.70 -0.08 -0.37 [grid] [f=70]
  o=41 v= 0.308331: -1.50 15.33 20.13 1.40 0.10 -0.30 [grid] [f=52]
  o=42 v= 0.331188: -0.45 15.90 20.22 0.22 -0.25 -0.01 [grid] [f=64]
  o=43 v= 0.310094: -1.65 15.22 19.95 1.58 -0.25 -0.16 [rand] [f=83]
  o=44 v= 0.309687: -1.65 15.32 20.09 1.60 -0.13 -0.22 [grid] [f=60]
  o=45 v= 0.307209: -1.63 15.07 20.12 1.59 0.13 -0.16 [grid] [f=66]
  o=46 v= 0.307871: -1.30 15.31 20.02 1.30 0.12 -0.06 [rand] [f=71]
  o=47 v= 0.308200: -1.59 15.01 20.13 1.63 0.08 -0.29 [grid] [f=64]
  o=48 v= 0.309270: -1.57 15.30 20.10 1.45 -0.14 -0.21 [grid] [f=66]
  o=49 v= 0.308250: -1.49 15.27 20.08 1.36 -0.08 -0.26 [grid] [f=67]
  o=50 v= 0.308963: -1.43 15.16 20.14 1.39 0.25 -0.14 [rand] [f=56]
  o=51 v= 0.307946: -1.53 15.11 20.02 1.64 0.09 -0.10 [rand] [f=83]
  o=52 v= 0.308512: -1.51 15.24 20.14 1.41 -0.10 -0.19 [grid] [f=77]
  o=53 v= 0.307580: -1.67 14.99 20.02 1.63 0.05 -0.11 [grid] [f=71]
  o=54 v= 0.308589: -1.56 15.06 20.11 1.48 -0.13 -0.03 [grid] [f=73]
  o=55 v= 0.309280: -1.39 15.36 20.08 1.52 -0.14 -0.37 [grid] [f=62]
  o=56 v= 0.308503: -1.35 15.31 20.00 1.32 -0.03 -0.41 [grid] [f=76]
  o=57 v= 0.309154: -1.48 15.10 20.20 1.53 -0.20 0.03 [grid] [f=63]
  o=58 v= 0.307935: -1.50 15.29 20.14 1.31 0.10 -0.27 [grid] [f=54]
  o=59 v= 0.308552: -1.54 15.32 20.20 1.35 0.02 -0.32 [grid] [f=62]
  o=60 v= 0.309565: -1.40 15.25 19.86 1.29 -0.27 -0.18 [grid] [f=72]
  o=61 v= 0.309012: -1.63 15.24 20.15 1.41 -0.18 -0.17 [grid] [f=55]
  o=62 v= 0.308314: -1.43 15.08 20.05 1.49 0.16 -0.05 [grid] [f=79]
  o=63 v= 0.309277: -1.42 15.38 20.08 1.40 -0.20 -0.28 [rand] [f=71]
  o=64 v= 0.309356: -1.54 15.24 20.14 1.61 -0.19 0.04 [grid] [f=83]
  o=65 v= 0.307848: -1.56 15.07 20.06 1.65 0.15 -0.15 [grid] [f=67]
  o=66 v= 0.309543: -1.41 15.41 20.06 1.46 -0.15 -0.26 [grid] [f=53]
  o=67 v= 0.310289: -1.63 15.38 19.95 1.68 -0.49 -0.15 [grid] [f=79]
  o=68 v= 0.309286: -1.63 14.93 19.80 1.70 -0.14 -0.17 [rand] [f=70]
  o=69 v= 0.307628: -1.55 15.06 20.06 1.64 0.09 -0.15 [grid] [f=66]
  o=70 v= 0.308379: -1.43 15.36 20.13 1.27 -0.15 -0.28 [grid] [f=61]
  o=71 v= 0.308384: -1.57 15.08 20.18 1.53 0.23 -0.17 [grid] [f=76]
  o=72 v= 0.310306: -1.59 15.26 20.08 1.49 -0.40 0.02 [grid] [f=74]
  o=73 v= 0.308260: -1.48 15.27 20.03 1.37 -0.05 -0.27 [grid] [f=78]
  o=74 v= 0.308935: -1.53 15.37 20.15 1.37 0.05 -0.23 [rand] [f=71]
  o=75 v= 0.310036: -1.36 15.30 20.17 1.22 0.34 0.09 [grid] [f=52]
  o=76 v= 0.312223: -1.33 15.23 20.37 1.23 0.29 0.04 [grid] [f=83]
  o=77 v= 0.307817: -1.68 14.96 20.10 1.62 0.16 -0.19 [grid] [f=61]
  o=78 v= 0.308932: -1.45 15.22 20.14 1.37 -0.14 0.16 [grid] [f=72]
  o=79 v= 0.309148: -1.47 15.20 20.12 1.61 -0.11 0.04 [grid] [f=69]
  o=80 v= 0.310337: -1.64 15.49 20.18 1.58 0.06 -0.28 [grid] [f=72]
  o=81 v= 0.307808: -1.62 15.05 20.10 1.64 0.13 -0.20 [rand] [f=61]
  o=82 v= 0.308319: -1.44 15.40 20.04 1.24 -0.11 -0.39 [grid] [f=64]
  o=83 v= 0.308659: -1.45 15.17 20.16 1.45 0.15 -0.39 [grid] [f=74]
  o=84 v= 0.309075: -1.64 15.33 20.12 1.50 -0.14 -0.09 [rand] [f=58]
  o=85 v= 0.332522: -0.64 15.50 19.69 0.15 -1.01 0.03 [grid] [f=60]
  o=86 v= 0.308552: -1.33 15.31 19.93 1.30 -0.02 0.03 [grid] [f=73]
  o=87 v= 0.308438: -1.35 15.30 19.98 1.15 0.09 0.02 [grid] [f=83]
- saving #10 for use with twobest
- skip #45 for twobest: too close to set #10
- skip # 4 for twobest: too close to set #10
- skip #53 for twobest: too close to set #10
- skip #24 for twobest: too close to set #10
- skip #69 for twobest: too close to set #10
- skip #34 for twobest: too close to set #10
- skip #81 for twobest: too close to set #10
- skip #77 for twobest: too close to set #10
- skip #65 for twobest: too close to set #10
- skip #46 for twobest: too close to set #10
- skip # 5 for twobest: too close to set #10
- skip #58 for twobest: too close to set #10
- skip #51 for twobest: too close to set #10
- skip #20 for twobest: too close to set #10
- skip #39 for twobest: too close to set #10
- skip #14 for twobest: too close to set #10
- skip #47 for twobest: too close to set #10
- skip #49 for twobest: too close to set #10
- skip # 1 for twobest: too close to set #10
- skip #73 for twobest: too close to set #10
- skip #31 for twobest: too close to set #10
- skip #27 for twobest: too close to set #10
- skip #62 for twobest: too close to set #10
- skip #82 for twobest: too close to set #10
- skip #41 for twobest: too close to set #10
- skip #17 for twobest: too close to set #10
- skip #70 for twobest: too close to set #10
- skip #71 for twobest: too close to set #10
- skip # 2 for twobest: too close to set #10
- skip #25 for twobest: too close to set #10
- skip # 7 for twobest: too close to set #10
- skip #87 for twobest: too close to set #10
- skip #56 for twobest: too close to set #10
- skip #52 for twobest: too close to set #10
- skip # 3 for twobest: too close to set #10
- skip #16 for twobest: too close to set #10
- skip #59 for twobest: too close to set #10
- skip #86 for twobest: too close to set #10
- skip #33 for twobest: too close to set #10
- skip #36 for twobest: too close to set #10
- skip #38 for twobest: too close to set #10
- skip #54 for twobest: too close to set #10
- skip #22 for twobest: too close to set #10
- skip #83 for twobest: too close to set #10
- skip # 0 for twobest: too close to set #10
- skip #78 for twobest: too close to set #10
- skip #74 for twobest: too close to set #10
- skip #50 for twobest: too close to set #10
- skip # 8 for twobest: too close to set #10
- skip #61 for twobest: too close to set #10
- skip # 6 for twobest: too close to set #10
- skip #32 for twobest: too close to set #10
- skip #84 for twobest: too close to set #10
- skip #79 for twobest: too close to set #10
- skip #57 for twobest: too close to set #10
- skip #37 for twobest: too close to set #10
- skip #18 for twobest: too close to set #10
- skip #12 for twobest: too close to set #10
- skip #48 for twobest: too close to set #10
- skip #63 for twobest: too close to set #10
- skip #55 for twobest: too close to set #10
- skip #68 for twobest: too close to set #10
- skip #64 for twobest: too close to set #10
- skip #26 for twobest: too close to set #10
- skip #15 for twobest: too close to set #10
- skip #66 for twobest: too close to set #10
- skip #60 for twobest: too close to set #10
- skip #21 for twobest: too close to set #10
- skip #44 for twobest: too close to set #10
- skip #11 for twobest: too close to set #10
- skip #40 for twobest: too close to set #10
- skip #29 for twobest: too close to set #10
- skip #35 for twobest: too close to set #10
- skip #75 for twobest: too close to set #10
- skip #43 for twobest: too close to set #10
- skip #30 for twobest: too close to set #10
- skip #67 for twobest: too close to set #10
- skip #72 for twobest: too close to set #10
- skip #80 for twobest: too close to set #10
- skip #19 for twobest: too close to set #10
- skip #13 for twobest: too close to set #10
- skip #23 for twobest: too close to set #10
- skip # 9 for twobest: too close to set #10
- skip #28 for twobest: too close to set #10
- skip #76 for twobest: too close to set #10
- skip #42 for twobest: too close to set #10
- skip #85 for twobest: too close to set #10
- Coarse startup search net CPU time = 0.0 s
  ++ Start refinement #1 on 2 coarse parameter sets
- Enter alignment setup routine
- Smoothing base; radius=2.37
- Smoothing source; radius=2.37
!source mask fill: ubot=70 usiz=180
- retaining old weight image
- using 54513 points from base image [use_all=2]
- Exit alignment setup routine
- histogram: source clip 105.932 … 437.262; base clip 256.176 … 933.135
- versus source range 0.0743793 … 415.448; base range 0 … 1186.43
47389 total points stored in 97 ‘TOHD(15.8702)’ bloks (0 duplicates)
*[#22260=0.290236] *[#22280=0.282163] *[#22282=0.281577] *[#22283=0.280476] *[#22286=0.280403] *[#22287=0.280152] *[#22288=0.279483] *[#22298=0.27762] *[#22300=0.276422] *[#22303=0.275735] *[#22304=0.274592] *[#22306=0.273336] *[#22309=0.273165] *[#22313=0.272964] *[#22315=0.271809] *[#22327=0.271804] *[#22328=0.271782] *[#22330=0.271636] *[#22331=0.271544] *[#22334=0.271507] *[#22335=0.2715] *[#22337=0.271489] *[#22338=0.271467] *[#22343=0.271464] *[#22347=0.271462] *[#22351=0.271402] *[#22352=0.271389] *[#22353=0.271335] *[#22356=0.271323] *[#22357=0.271296] *[#22358=0.271268]
- param set #1 has cost=0.271268 [o=10 t=0]
– Parameters = -1.5497 15.1164 20.2084 1.4938 -0.0676 -0.3731 0.9927 0.9950 0.9851 -0.0061 0.0021 -0.0036
- param set #2 has cost=0.272636 [o=-1 t=-1]
– Parameters = -1.5082 15.2797 20.1000 1.4839 -0.1318 -0.2518 0.9915 0.9922 0.9940 -0.0005 0.0007 -0.0012
++ Start refinement #2 on 2 coarse parameter sets
- Enter alignment setup routine
- Smoothing base; radius=1.84
- Smoothing source; radius=1.84
!source mask fill: ubot=70 usiz=180
- retaining old weight image
- using 54513 points from base image [use_all=2]
- Exit alignment setup routine
- histogram: source clip 106.996 … 439.585; base clip 256.658 … 944.475
- versus source range 0 … 415.558; base range 0 … 1188.15
47358 total points stored in 98 ‘TOHD(15.8002)’ bloks (0 duplicates)
*[#22460=0.257511] *[#22499=0.257455] *[#22502=0.257419] *[#22503=0.257407] *[#22505=0.257391] *[#22506=0.257376] *[#22507=0.25733] *[#22508=0.257297] *[#22511=0.257273]
- param set #1 has cost=0.257273 [o=10 t=0]
– Parameters = -1.5452 15.1036 20.2542 1.4893 -0.0981 -0.3709 0.9936 0.9950 0.9851 -0.0059 0.0021 -0.0038
*[#22584=0.257218] *[#22585=0.257063] *[#22586=0.25703] *[#22588=0.256921] *[#22589=0.25677] *[#22592=0.256724] *[#22594=0.256685] *[#22596=0.256666] *[#22597=0.25663] *[#22600=0.256617] *[#22601=0.256616] *[#22604=0.2566] *[#22610=0.256549] *[#22613=0.256507] *[#22614=0.256467] *[#22617=0.25644] *[#22621=0.256433] *[#22624=0.256357] *[#22626=0.256356] *[#22627=0.25635] *[#22631=0.256316]
- param set #2 has cost=0.256316 [o=-1 t=-1]
– Parameters = -1.5248 15.0953 20.1555 1.5216 -0.2228 -0.2726 0.9918 0.9961 0.9922 -0.0018 0.0028 -0.0047
++ Start refinement #3 on 2 coarse parameter sets
- Enter alignment setup routine
- Smoothing base; radius=1.43
- Smoothing source; radius=1.43
!source mask fill: ubot=70 usiz=180
- retaining old weight image
- using 54513 points from base image [use_all=2]
- Exit alignment setup routine
- histogram: source clip 107.039 … 440.653; base clip 257.01 … 950.393
- versus source range 0 … 415.463; base range 0 … 1189.88
47481 total points stored in 99 ‘TOHD(15.7577)’ bloks (0 duplicates)
*[#22641=0.255089] *[#22665=0.254592] *[#22668=0.254349] *[#22673=0.25429] *[#22677=0.254223] *[#22682=0.254103] *[#22683=0.254037] *[#22686=0.253579] *[#22691=0.253572] *[#22695=0.253448] *[#22698=0.253197] *[#22701=0.253068] *[#22704=0.252627] *[#22705=0.252354] *[#22706=0.251973] *[#22709=0.251803] *[#22712=0.251676] *[#22719=0.25167] *[#22721=0.251382] *[#22723=0.251356] *[#22726=0.251341] *[#22728=0.251317] *[#22731=0.251182] *[#22739=0.251164] *[#22741=0.251152] *[#22748=0.251151] *[#22753=0.25114] *[#22756=0.251139] *[#22758=0.251137] *[#22760=0.251119] *[#22761=0.251116]
- param set #1 has cost=0.251116 [o=10 t=0]
– Parameters = -1.5316 15.0934 20.1594 1.5067 -0.3817 -0.3735 0.9923 0.9958 0.9931 -0.0081 0.0049 -0.0084
- param set #2 has cost=0.252752 [o=-1 t=-1]
– Parameters = -1.5148 15.0795 20.1461 1.5943 -0.2784 -0.3270 0.9923 0.9954 0.9939 -0.0033 0.0055 -0.0050
- Total coarse refinement net CPU time = 0.0 s; 599 funcs
  ++ *** Fine pass begins ***
- Enter alignment setup routine
- Smoothing base; radius=1.00
- Smoothing source; radius=1.00
!source mask fill: ubot=70 usiz=180
- retaining old weight image
- Exit alignment setup routine
  ++ Picking best parameter set out of 3 cases
- histogram: source clip 107.08 … 441.966; base clip 257.01 … 950.393
- versus source range 0 … 415.712; base range 0 … 1190.51
46998 total points stored in 98 ‘TOHD(15.7242)’ bloks (0 duplicates)
*[#22865=0.245173] + - cost(#1)=0.245173 * [o=10 t=0]
– Parameters = -1.5316 15.0934 20.1594 1.5067 -0.3817 -0.3735 0.9923 0.9958 0.9931 -0.0081 0.0049 -0.0084
- cost(#2)=0.246763 [o=-1 t=-1]
– Parameters = -1.5148 15.0795 20.1461 1.5943 -0.2784 -0.3270 0.9923 0.9954 0.9939 -0.0033 0.0055 -0.0050
- cost(#3)=0.524277 [o=-2 t=-2]
– Parameters = -1.0462 16.0244 16.6902 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
-num_rtb 99 ==> refine all 3 cases
*[#22919=0.244865] *[#22922=0.244762] *[#22930=0.244724] *[#22932=0.244569] *[#22935=0.244529] *[#22951=0.244524]
- cost(#1)=0.244524 * [o=10 t=0]
– Parameters = -1.5274 15.1220 20.1534 1.5278 -0.4911 -0.3475 0.9921 0.9955 0.9939 -0.0091 0.0050 -0.0090
- cost(#2)=0.245692 [o=-1 t=-1]
– Parameters = -1.4938 15.1445 20.1417 1.4982 -0.2933 -0.3458 0.9927 0.9943 0.9945 -0.0110 0.0060 -0.0054
- cost(#3)=0.251519 [o=-2 t=-2]
– Parameters = -1.4477 15.0460 20.0957 1.6578 0.0596 -0.1043 0.9940 0.9942 0.9947 -0.0001 -0.0004 0.0010
- case #1 [o=10 t=0] is now the best
- Initial cost = 0.244524
- Initial fine Parameters = -1.5274 15.1220 20.1534 1.5278 -0.4911 -0.3475 0.9921 0.9955 0.9939 -0.0091 0.0050 -0.0090
  *[#23337=0.244513] *[#23338=0.244488] *[#23345=0.24445] *[#23362=0.244441] *[#23363=0.244436] *[#23378=0.244433] *[#23379=0.244427] *[#23393=0.244426] *[#23397=0.244424] *[#23404=0.244418] *[#23413=0.244414] *[#23415=0.24441] *[#23425=0.244404]
- Finalish cost = 0.244404 ; 180 funcs
- ini Finalish Parameters = -1.5277 15.1135 20.1434 1.5196 -0.4813 -0.3353 0.9923 0.9956 0.9941 -0.0090 0.0050 -0.0089
- histogram: source clip 107.045 … 441.986; base clip 257.01 … 950.393
- versus source range 0 … 415.712; base range 0 … 1190.51
  *[#23700=0.244404]
- Final cost = 0.244404 ; 267 funcs
Final fine fit Parameters:
x-shift= -1.5277 y-shift= 15.1137 z-shift= 20.1433 … enorm= 25.2291 mm
z-angle= 1.5195 x-angle= -0.4814 y-angle= -0.3353 … total= 1.6301 deg
x-scale= 0.9923 y-scale= 0.9956 z-scale= 0.9941 … vol3D= 0.9821=(0.9940)^3 [base about same as source]
y/x-shear= -0.0090 z/x-shear= 0.0050 z/y-shear= -0.0089
- Fine net CPU time = 0.0 s
  ++ Computing output image
  ++ image warp: parameters = -1.5277 15.1137 20.1433 1.5195 -0.4814 -0.3353 0.9923 0.9956 0.9941 -0.0090 0.0050 -0.0089
  ++ Unloading unneeded data
  ++ Wrote -1Dmatrix_save ./MPRAGE_sag_CM_al_e2a_only_mat.aff12.1D
  ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 35.9
  ++ ###########################################################
  ++ # PLEASE check results VISUALLY for alignment quality #
  ++ ###########################################################
  #Script is running (command trimmed):
  rm ./MPRAGE_sag_CM_al+orig.HEAD
  #Script is running (command trimmed):
  rm ./MPRAGE_sag_CM_al+orig.BRIK.gz
  #Script is running (command trimmed):
  cat_matvec -ONELINE ./MPRAGE_sag_CM_al_e2a_only_mat.aff12.1D ./__tt_MPRAGE_sag_CM_ns_shft_I.1D -I > ./MPRAGE_sag_CM_al_mat.aff12.1D
  #++ Combining anat to epi and oblique transformations
  #Script is running (command trimmed):
  3dAllineate -base ./__tt_sw3_CM_tsh_vr_ts_ns+orig -1Dmatrix_apply ./MPRAGE_sag_CM_al_mat.aff12.1D -prefix ./MPRAGE_sag_CM_al -input ./__tt_MPRAGE_sag_CM_ns+orig -master BASE -mast_dxyz 1.000000 -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -source_automask+4 -twobest 11 -twopass -VERB -maxrot 45 -maxshf 40 -fineblur 1 -source_automask+2
  ++ 3dAllineate: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
  ++ Authored by: Zhark the Registrator
  ++ Source dataset: ./__tt_MPRAGE_sag_CM_ns+orig.HEAD
  ++ Base dataset: ./__tt_sw3_CM_tsh_vr_ts_ns+orig.HEAD
  ++ Loading datasets into memory
  ++ largeness ==> set -twobest 29
  ++ NOTE: base and source coordinate systems have different handedness

  Orientations: base=Right handed (RAI); 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.

++ base center of mass = 32.232 34.227 18.379 (index)

source center of mass = 151.833 106.672 88.684 (index)
source-target CM = -0.357 6.562 41.033 (xyz)
*+ WARNING: center of mass shifts (-cmass) are turned off, but would be TERRIBLY large!
*+ WARNING: - at least one is more than 50% of search range

   -cmass x y z shifts =   -0.357    6.562   41.033

shift search range is +/- = 61.617 61.617 32.742

                             0.6%    10.7%   125.3%

Range param#4 [z-angle] = -6.000000 … 6.000000 center = 0.000000
Range param#5 [x-angle] = -6.000000 … 6.000000 center = 0.000000
Range param#6 [y-angle] = -6.000000 … 6.000000 center = 0.000000
Range param#1 [x-shift] = -10.000000 … 10.000000 center = 0.000000
Range param#2 [y-shift] = -10.000000 … 10.000000 center = 0.000000
Range param#3 [z-shift] = -10.000000 … 10.000000 center = 0.000000
Range param#4 [z-angle] = -45.000000 … 45.000000 center = 0.000000
Range param#5 [x-angle] = -45.000000 … 45.000000 center = 0.000000
Range param#6 [y-angle] = -45.000000 … 45.000000 center = 0.000000
Range param#1 [x-shift] = -40.000000 … 40.000000 center = 0.000000
Range param#2 [y-shift] = -40.000000 … 40.000000 center = 0.000000
Range param#3 [z-shift] = -40.000000 … 40.000000 center = 0.000000
++ Final parameter search ranges:
```
  x-shift =  -40.000 ..   40.000
```
```
  y-shift =  -40.000 ..   40.000
```
```
  z-shift =  -40.000 ..   40.000
```
```
  z-angle =  -45.000 ..   45.000
```
```
  x-angle =  -45.000 ..   45.000
```
```
  y-angle =  -45.000 ..   45.000
```
```
  x-scale =    0.711 ..    1.406
```
```
  y-scale =    0.711 ..    1.406
```
```
  z-scale =    0.711 ..    1.406
```
```
y/x-shear =   -0.111 ..    0.111
```
```
z/x-shear =   -0.111 ..    0.111
```
```
z/y-shear =   -0.111 ..    0.111
```

++ changing output grid spacing to 1.0000 mm
++ OpenMP thread count = 15
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU to here=0.0 s]

- Enter alignment setup routine
- copying base image
- copying source image
- no weight image
- using 11 points from base image [use_all=0]
- Exit alignment setup routine
  ++ using -1Dmatrix_apply
  ++ Computing output image
  ++ image warp: parameters = -0.0354 0.9950 -0.0084 50.1188 0.0008 0.0006 -0.9942 158.8962 0.9919 0.0264 0.0058 -13.2458
  ++ Unloading unneeded data
  ++ 3dAllineate: total CPU time = 0.0 sec Elapsed = 0.5
  ++ ###########################################################

++ ***********************************************************
*+ WARNING: -cmass was turned off, but might have been needed

      Please check your results - PLEASE PLEASE PLEASE

++ ***********************************************************
#++ Creating final output: anat data aligned to epi

copy is not necessary

#++ Saving history
#Script is running (command trimmed):
3dNotes -h “align_epi_anat.py -verb 5 -anat MPRAGE_sag_CM+orig -epi
sw3_CM+orig -anat2epi -ginormous_move -cost lpc+ -epi_base mean
-child_epi sw1_CM+orig sw2_CM+orig sw4_CM+orig sw5_CM+orig sw6_CM+orig
-tshift_opts ‘-ignore 4’ -output_dir
/home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func
-save_vr -suffix _al -overwrite”
./MPRAGE_sag_CM_al+orig

#++ Creating final output: time series volume-registered epi
copying from dataset /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw3_CM_tsh_vr+orig to /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw3_CM_vr+orig
#Script is running (command trimmed):
rm ./sw3_CM_vr+orig.HEAD
#Script is running (command trimmed):
rm ./sw3_CM_vr+orig.BRIK.gz
#Script is running (command trimmed):
3dcopy ./sw3_CM_tsh_vr+orig sw3_CM_vr
++ 3dcopy: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
#++ Parent /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw3_CM+orig: Child: /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2002_S40/func/sw1_CM+orig
#Script is running (command trimmed):
3dAttribute TAXIS_OFFSETS ./sw1_CM+orig
#++ Correcting for slice timing
#Script is running (command trimmed):
3dTshift -prefix ./__tt_sw1_CM_tsh -ignore 4 ./sw1_CM+orig
++ 3dTshift: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ updating time offset to 0.971428
#Script is running (command trimmed):
rm ./sw1_CM_tsh_vr+orig.HEAD
#Script is running (command trimmed):
rm ./sw1_CM_tsh_vr+orig.BRIK.gz
#++ Volume registration for epi data
#Script is running (command trimmed):
3dvolreg -1Dfile ./sw1_CM_tsh_vr_motion.1D -1Dmatrix_save ./sw1_CM_tsh_vr_mat.aff12.1D -prefix ./sw1_CM_tsh_vr -base ./sw3_CM+orig’[mean]’ -cubic ./__tt_sw1_CM_tsh+orig
++ 3dvolreg: AFNI version=AFNI_23.0.02 (Jan 24 2023) [64-bit]
++ Authored by: RW Cox
** ERROR: selector syntax error 5 ‘mean]’
** ERROR: bad sub-brick selector [mean]
** FATAL ERROR: Couldn’t open -base dataset ./sw3_CM+orig[mean]
** Program compile date = Jan 24 2023
#**ERROR Could not do volume registration
** ERROR - script failed

ptaylor · March 9, 2023, 12:37pm

Thanks for that full output.

I am now running this command with “-child_epi …” and “-tshift_opts …”, and still not getting an error:


align_epi_anat.py         -verb 5                                            \
    -anat         FT_anat+orig.HEAD                                          \
    -epi          pb00.FT.r01.tcat+orig.HEAD                                 \
    -anat2epi                                                                \
    -giant_move                                                              \
    -cost         lpc+                                                       \
    -epi_base     mean                                                       \
    -child_epi    pb00.FT.r02.tcat+orig pb00.FT.r03.tcat+orig     \
    -tshift_opts  '-ignore 4'                                                \
    -output_dir   ./odir                                                     \
    -save_vr                                                                 \
    -suffix       _al                                                        \
    -overwrite \
    |& tee out_my_aea.txt

However, I think the different must be that you actually have slice shifts to apply to your data, and the EPIs that I have do not have those. I will ping you to get your datasets, if that is OK, to use those directly, but I suspect that is where the error is popping up; I think the ‘mean’ label is being misapplied there.

–pt

wgraves · March 9, 2023, 2:34pm

Thanks for looking into that! I’ll keep an eye out for an email and will be happy to follow up.