OK, I tried this:
align_epi_anat.py -giant_move -AddEdge -epi2anat -anat_has_skull no -Allineate_opts -warp shift_rotate -anat refvol.lpcregister+orig -epi movvol.lpcregister+orig -epi_base 0
but it gives me results that are identical to when I do not use -Allineate_opts. The terminal output (below), implies that 12 dof is being used ("12 free parameters"). There are a few errors (including one "FATAL"), but at the end it says "Finished alignment successfully".
Any more hints?
thanks
doug
align_epi_anat.py -giant_move -AddEdge -epi2anat -anat_has_skull no -Allineate_opts -warp shift_rotate -anat refvol.lpcregister+orig -epi movvol.lpcregister+orig -epi_base 0
#++ align_epi_anat version: 1.17
#Script is running (command trimmed):
3dAttribute DELTA movvol.lpcregister+orig
#++ Spacing for EPI to tlrc alignment is 3.437500 mm
#Script is running (command trimmed):
3dAttribute DELTA refvol.lpcregister+orig
#++ Spacing for anat to EPI deobliquing is 1.000000 mm
#++ Removing all the temporary files
#Script is running:
rm -f __tt_movvol.lpcregister*
#Script is running:
rm -f __tt_refvol.lpcregister*
#Script is running (command trimmed):
3dcopy refvol.lpcregister+orig __tt_refvol.lpcregister
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
#Script is running (command trimmed):
3dinfo __tt_refvol.lpcregister+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /autofs/space/crash_001/users/greve/lpc/tmp.lpc/__tt_refvol.lpcregister+orig is not oblique
#Script is running (command trimmed):
3dinfo movvol.lpcregister+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /autofs/space/crash_001/users/greve/lpc/tmp.lpc/movvol.lpcregister+orig is ***oblique****
#++ Matching obliquity of anat to epi
#++ Matching obliquity of anat to epi
#Script is running (command trimmed):
3dWarp -verb -card2oblique movvol.lpcregister+orig -prefix __tt_refvol.lpcregister_ob -newgrid 1.000000 __tt_refvol.lpcregister+orig | \grep -A 4 '# mat44 Obliquity Transformation ::' > __tt_refvol.lpcregister_obla2e_mat.1D
++ 3dWarp: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: RW Cox
++ Output dataset ./__tt_refvol.lpcregister_ob+orig.BRIK
#Script is running (command trimmed):
3dAttribute TAXIS_OFFSETS movvol.lpcregister+orig
#++ Can not do time shifting of slices. Data is already time shifted
#++ Skipping time series volume registration. Must have more than a single sub-brick.
#++ using 0th sub-brick because only one found
#Script is running (command trimmed):
3dbucket -prefix __tt_movvol.lpcregister_ts movvol.lpcregister+orig'[0]'
++ 3dbucket: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./movvol.lpcregister+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:./movvol.lpcregister+orig.BRIK is 13.100002 degrees from plumb.
#++ resampling epi to match anatomical data
#Script is running (command trimmed):
3dresample -master __tt_refvol.lpcregister_ob+orig -prefix __tt_movvol.lpcregister_ts_rs -inset __tt_movvol.lpcregister_ts+orig'' -rmode Cu
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./__tt_movvol.lpcregister_ts+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:./__tt_movvol.lpcregister_ts+orig.BRIK is 13.100002 degrees from plumb.
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dSkullStrip -input __tt_movvol.lpcregister_ts_rs+orig -prefix __tt_movvol.lpcregister_ts_rs_ns
The intensity in the output dataset is a modified version
of the intensity in the input volume.
To obtain a masked version of the input with identical values inside
the brain, you can either use 3dSkullStrip's -orig_vol option
or run the following command:
3dcalc -a __tt_movvol.lpcregister_ts_rs+orig -b __tt_movvol.lpcregister_ts_rs_ns+orig -expr 'a*step(b)' \
-prefix __tt_movvol.lpcregister_ts_rs_ns_orig_vol
to generate a new masked version of the input.
#++ Computing weight mask
#Script is running (command trimmed):
3dBrickStat -automask -percentile 90.000000 1 90.000000 __tt_movvol.lpcregister_ts_rs_ns+orig
#++ Applying threshold of 3193.000000 on /autofs/space/crash_001/users/greve/lpc/tmp.lpc/__tt_movvol.lpcregister_ts_rs_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix __tt_movvol.lpcregister_ts_rs_ns_wt -a __tt_movvol.lpcregister_ts_rs_ns+orig -expr 'min(1,(a/3193.000000))'
++ 3dcalc: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./__tt_movvol.lpcregister_ts_rs_ns_wt+orig.BRIK
#++ Aligning anatomical data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix __tt_refvol.lpcregister_ob_al_wtal -weight __tt_movvol.lpcregister_ts_rs_ns_wt+orig -source __tt_refvol.lpcregister_ob+orig -prefix __tt_refvol.lpcregister_ob_temp_al -base __tt_movvol.lpcregister_ts_rs_ns+orig -cmass -1Dmatrix_save refvol.lpcregister_al_e2a_only_mat.aff12.1D -master SOURCE -twopass -VERB -maxrot 45 -maxshf 40
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: Emperor Zhark
++ Loading datasets
++ Zero-pad: not needed
++ 1547968 voxels [6.4%] in weight mask
++ Output dataset ./__tt_refvol.lpcregister_ob_al_wtal+orig.BRIK
++ Number of points for matching = 727544
++ Local correlation: blok type = 'RHDD(6.54321)'
++ base center of mass = 132.295 188.844 232.746 (index)
++ source center of mass = 125.222 159.598 175.245 (index)
++ source-target CM = -7.073 -29.246 -57.500 (xyz)
++ center of mass shifts = -7.073 -29.246 -57.500
++ shift param auto-range: -88.9..74.8 -127.8..69.3 -156.0..41.0
+ Range param#4 [z-angle] = -45.000000 .. 45.000000
+ Range param#5 [x-angle] = -45.000000 .. 45.000000
+ Range param#6 [y-angle] = -45.000000 .. 45.000000
+ Range param#1 [x-shift] = -47.072838 .. 32.927162
+ Range param#2 [y-shift] = -69.245636 .. 10.754364
+ Range param#3 [z-shift] = -97.500458 .. -17.500458
+ 12 free parameters
++ Normalized convergence radius = 0.000423
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ Memory usage now = 218603502 (219 million): about to start alignment loop
++ ========== sub-brick #0 ========== [total CPU=1.7 s]
++ Start coarse pass
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - Smoothing base; radius=2.22
+ - Smoothing source; radius=2.22
+ - copying weight image
+ - using 103197 points from base image
+ * Exit alignment setup routine
+ - Search for coarse starting parameters
+ 93430 total points stored in 487 'RHDD(6.9102)' bloks
+ - Testing 95*64 params:**.*...*...**......*.
+ - best 15 costs found:
0 v=-0.092655: 2.75 -54.00 -68.88 3.10 34.36 2.55
1 v=-0.085256: -20.41 -42.58 -44.17 -30.00 -15.00 15.00
2 v=-0.083627: -20.49 -6.56 -26.16 -4.37 -20.12 -15.12
3 v=-0.082202: 19.59 -55.91 -70.83 -15.00 15.00 30.00
4 v=-0.079261: 6.26 -55.91 -30.83 -15.00 30.00 15.00
5 v=-0.078987: 6.35 -51.93 -26.16 4.37 20.12 -15.12
6 v=-0.077755: 7.13 -38.70 -52.66 15.99 13.53 -29.93
7 v=-0.077717: -36.09 -2.10 -23.89 -7.44 -27.42 25.63
8 v=-0.076800: 6.26 -15.91 -30.83 -30.00 -15.00 -15.00
9 v=-0.076584: -33.74 -2.58 -30.83 30.00 15.00 -30.00
10 v=-0.075614: -1.09 -25.84 -32.97 29.81 4.26 23.54
11 v=-0.074602: -21.28 -38.70 -52.66 -15.99 13.53 29.93
12 v=-0.073288: -20.41 -55.91 -44.17 15.00 -15.00 -30.00
13 v=-0.073272: -18.67 -33.80 -53.61 -24.53 29.49 -26.10
14 v=-0.073059: 19.59 -55.91 -30.83 30.00 15.00 -15.00
+ - costs of the above after a little optimization:
0 v=-0.133381: -2.84 -47.40 -66.92 -1.69 28.76 3.50
1 v=-0.111977: -22.91 -42.97 -44.23 -29.11 -16.10 16.01
* 2 v=-0.187323: -22.61 -13.83 -24.24 -6.83 -17.10 -14.57
3 v=-0.113295: 20.62 -59.94 -71.51 -12.51 16.01 29.73
4 v=-0.085423: 6.72 -55.90 -29.61 -14.86 30.57 15.00
5 v=-0.098904: 4.56 -51.50 -27.74 1.67 19.70 -15.33
6 v=-0.124250: 7.22 -35.74 -54.25 13.59 9.36 -25.81
7 v=-0.089158: -34.84 -1.48 -23.62 -5.48 -26.96 27.86
8 v=-0.109078: 6.26 -14.44 -26.95 -28.62 -17.17 -15.14
9 v=-0.115390: -40.93 -1.61 -27.36 34.14 10.90 -38.78
10 v=-0.119187: 0.83 -20.54 -29.35 28.58 4.06 27.00
11 v=-0.083757: -21.63 -34.29 -52.62 -15.60 13.67 29.70
12 v=-0.091877: -20.61 -58.30 -41.77 15.51 -14.76 -30.44
13 v=-0.106900: -12.83 -33.69 -48.31 -30.31 29.97 -21.80
14 v=-0.111705: 15.21 -63.40 -28.66 28.09 14.98 -18.72
+ - save # 2 for twobest
+ - save # 0 for twobest
+ - save # 6 for twobest
+ - save #10 for twobest
+ - save # 9 for twobest
+ - save # 3 for twobest
+ - save # 1 for twobest
+ - Search CPU time = 63.3 s
++ Start refinement #1 on 5 coarse parameter sets
+ * Enter alignment setup routine
+ - Smoothing base; radius=1.57
+ - Smoothing source; radius=1.57
+ - retaining old weight image
+ - using 154795 points from base image
+ * Exit alignment setup routine
+ 137742 total points stored in 504 'RHDD(6.7292)' bloks
+ - param set #1 has cost=-0.171093
+ -- Parameters = -22.9623 -15.2616 -25.9056 -6.6341 -15.7989 -14.1111 1.0013 0.9750 1.0042 0.0029 -0.0111 0.0021
+ - param set #2 has cost=-0.141329
+ -- Parameters = -5.2683 -49.5758 -67.4261 -1.7314 28.1795 2.3618 1.0053 0.9955 1.0106 0.0013 -0.0041 -0.0032
+ - param set #3 has cost=-0.117655
+ -- Parameters = 7.7796 -38.9886 -52.9890 14.4751 11.9671 -24.9863 0.9896 0.9214 0.9873 0.0064 0.0158 -0.0000
+ - param set #4 has cost=-0.096947
+ -- Parameters = 1.0464 -19.8319 -28.6494 28.3589 4.3498 27.6193 0.9966 0.9902 0.9996 -0.0002 -0.0004 0.0003
+ - param set #5 has cost=-0.622879
+ -- Parameters = -6.5426 -29.6330 -50.7839 -0.0003 0.1535 -0.0637 1.0011 0.9963 1.0027 0.0019 0.0004 -0.0011
+ - sorting parameter sets by cost
+ -- scanning for distances from #1
+ --- dist(#2,#1) = 0.311
+ --- dist(#3,#1) = 0.311
+ --- dist(#4,#1) = 0.277
+ --- dist(#5,#1) = 0.315
++ Start refinement #2 on 5 coarse parameter sets
+ * Enter alignment setup routine
+ - Smoothing base; radius=1.11
+ - Smoothing source; radius=1.11
+ - retaining old weight image
+ - using 232192 points from base image
+ * Exit alignment setup routine
+ 166956 total points stored in 351 'RHDD(6.63686)' bloks
+ - param set #1 has cost=-0.595183
+ -- Parameters = -6.5786 -29.6498 -50.7915 0.1094 0.4057 0.0046 1.0008 0.9861 1.0038 0.0013 0.0003 -0.0018
+ - param set #2 has cost=-0.140392
+ -- Parameters = -23.3387 -15.6342 -26.1787 -6.7214 -15.2315 -14.5023 1.0182 0.9688 0.9979 0.0067 -0.0125 0.0051
+ - param set #3 has cost=-0.099967
+ -- Parameters = -7.4850 -49.6082 -68.7474 -3.4013 28.1449 1.3345 1.0169 0.9871 1.0110 0.0004 -0.0080 -0.0204
+ - param set #4 has cost=-0.102438
+ -- Parameters = 7.7449 -39.1207 -52.9972 14.6718 12.6327 -24.7906 0.9873 0.9132 0.9789 0.0190 0.0009 -0.0096
+ - param set #5 has cost=-0.060786
+ -- Parameters = 1.9760 -23.7981 -29.9846 27.3643 6.8730 28.3262 0.9953 0.9894 0.9974 0.0024 0.0010 0.0051
+ - sorting parameter sets by cost
+ -- scanning for distances from #1
+ --- dist(#2,#1) = 0.308
+ --- dist(#3,#1) = 0.276
+ --- dist(#4,#1) = 0.308
+ --- dist(#5,#1) = 0.315
++ Start refinement #3 on 5 coarse parameter sets
+ * Enter alignment setup routine
+ - Smoothing base; radius=0.79
+ - Smoothing source; radius=0.79
+ - retaining old weight image
+ - using 348288 points from base image
+ * Exit alignment setup routine
+ 268224 total points stored in 545 'RHDD(6.5902)' bloks
+ - param set #1 has cost=-0.623621
+ -- Parameters = -6.4861 -29.9119 -50.9391 0.0863 0.5270 -0.0246 1.0015 0.9764 1.0054 0.0024 -0.0017 -0.0102
+ - param set #2 has cost=-0.128688
+ -- Parameters = -23.1267 -15.0400 -29.7212 -7.2578 -15.1646 -12.7716 1.0260 0.9657 1.0063 0.0052 -0.0146 0.0036
+ - param set #3 has cost=-0.081996
+ -- Parameters = 9.2403 -38.5075 -52.1215 14.7105 13.6778 -24.4775 0.9825 0.9169 0.9760 0.0207 0.0061 -0.0104
+ - param set #4 has cost=-0.103912
+ -- Parameters = -7.2830 -50.1495 -68.5817 -2.8645 28.0892 1.1437 1.0110 0.9883 1.0128 0.0042 -0.0134 -0.0411
+ - param set #5 has cost=-0.068470
+ -- Parameters = 3.4262 -22.9624 -29.5950 27.8616 7.0665 28.6391 1.0238 0.9909 0.9897 0.0088 0.0062 0.0155
+ - sorting parameter sets by cost
+ -- scanning for distances from #1
+ --- dist(#2,#1) = 0.265
+ --- dist(#3,#1) = 0.306
+ --- dist(#4,#1) = 0.272
+ --- dist(#5,#1) = 0.318
+ - Total coarse refinement CPU time = 32.2 s; 1463 funcs
++ *** Fine pass begins ***
+ * Enter alignment setup routine
+ - retaining old weight image
+ - using 727544 points from base image
+ * Exit alignment setup routine
++ Picking best parameter set out of 6 cases
+ 661804 total points stored in 1342 'RHDD(6.54321)' bloks
+ - cost(#1)=-0.668107 *
+ -- Parameters = -6.4861 -29.9119 -50.9391 0.0863 0.5270 -0.0246 1.0015 0.9764 1.0054 0.0024 -0.0017 -0.0102
+ - cost(#2)=-0.074110
+ -- Parameters = -23.1267 -15.0400 -29.7212 -7.2578 -15.1646 -12.7716 1.0260 0.9657 1.0063 0.0052 -0.0146 0.0036
+ - cost(#3)=-0.074815
+ -- Parameters = -7.2830 -50.1495 -68.5817 -2.8645 28.0892 1.1437 1.0110 0.9883 1.0128 0.0042 -0.0134 -0.0411
+ - cost(#4)=-0.031043
+ -- Parameters = 9.2403 -38.5075 -52.1215 14.7105 13.6778 -24.4775 0.9825 0.9169 0.9760 0.0207 0.0061 -0.0104
+ - cost(#5)=-0.040484
+ -- Parameters = 3.4262 -22.9624 -29.5950 27.8616 7.0665 28.6391 1.0238 0.9909 0.9897 0.0088 0.0062 0.0155
+ - cost(#6)=-0.063811
+ -- Parameters = -7.0728 -29.2456 -57.5005 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000
+ -num_rtb 99 ==> refine all 6 cases
+ - cost(#1)=-0.679846 *
+ -- Parameters = -6.4165 -30.0052 -51.1228 0.0551 0.5533 0.0637 1.0003 0.9833 1.0041 0.0028 -0.0007 -0.0102
+ - cost(#2)=-0.127597
+ -- Parameters = -18.2570 -16.1057 -31.3415 -6.1845 -15.3531 -5.1371 1.0395 0.9757 0.9875 -0.0153 -0.0125 0.0028
+ - cost(#3)=-0.109712
+ -- Parameters = -4.2681 -44.7143 -64.4962 -2.4968 25.4732 2.2917 1.0233 0.9776 1.0144 -0.0003 -0.0163 -0.0576
+ - cost(#4)=-0.041403
+ -- Parameters = 9.5656 -38.0525 -51.9028 15.3882 9.7687 -23.9378 0.9764 0.8990 0.9691 0.0195 0.0129 -0.0100
+ - cost(#5)=-0.053811
+ -- Parameters = 5.7667 -24.8049 -30.8560 27.4441 9.6505 32.1679 1.0482 0.9994 1.0153 0.0194 -0.0075 0.0026
+ - cost(#6)=-0.676450
+ -- Parameters = -6.4255 -30.6011 -50.8531 0.0626 1.1317 0.0712 1.0006 0.9904 1.0005 0.0028 0.0036 -0.0019
+ - case #1 is now the best
+ - Initial cost = -0.679846
+ - Initial fine Parameters = -6.4165 -30.0052 -51.1228 0.0551 0.5533 0.0637 1.0003 0.9833 1.0041 0.0028 -0.0007 -0.0102
+ - Finalish cost = -0.682084 ; 237 funcs
+ - Final cost = -0.682249 ; 88 funcs
+ Final fine fit Parameters = -6.3833 -29.7502 -51.0992 0.0659 0.4042 0.0948 1.0009 0.9879 1.0044 0.0032 0.0016 -0.0138
+ - Fine CPU time = 55.2 s
++ Computing output image
++ image warp: parameters = -6.3833 -29.7502 -51.0992 0.0659 0.4042 0.0948 1.0009 0.9879 1.0044 0.0032 0.0016 -0.0138
++ Memory usage now = 575811078 (576 million): end of sub-brick alignment
++ Memory usage now = 65821302 (66 million): end of sub-brick loop (after cleanup)
++ Output dataset ./__tt_refvol.lpcregister_ob_temp_al+orig.BRIK
++ Memory usage now = 41537499 (42 million): after writing output dataset
++ Wrote -1Dmatrix_save refvol.lpcregister_al_e2a_only_mat.aff12.1D
++ total CPU time = 158.1 sec Elapsed = 166.2
++ Memory usage now = 2699947 (2.7 million): end of program (after final cleanup)
++ ###########################################################
#Script is running:
cat_matvec -ONELINE refvol.lpcregister_al_e2a_only_mat.aff12.1D __tt_refvol.lpcregister_obla2e_mat.1D -I > refvol.lpcregister_al_mat.aff12.1D
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base __tt_movvol.lpcregister_ts_rs_ns+orig -1Dmatrix_apply refvol.lpcregister_al_mat.aff12.1D -prefix refvol.lpcregister_al -input __tt_refvol.lpcregister+orig -master SOURCE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: Emperor Zhark
++ Loading datasets
*+ WARNING: base and source datasets have different handedness!
*+ WARNING: Alignment will proceed, but examine results carefully!
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU=0.1 s]
++ Output dataset ./refvol.lpcregister_al+orig.BRIK
++ total CPU time = 2.7 sec Elapsed = 3.0
++ ###########################################################
#++ Aligning /autofs/space/crash_001/users/greve/lpc/tmp.lpc/movvol.lpcregister+orig to anat
#++ Inverting anat to epi matrix
#Script is running:
cat_matvec -ONELINE __tt_refvol.lpcregister_obla2e_mat.1D refvol.lpcregister_al_e2a_only_mat.aff12.1D -I > movvol.lpcregister_al_mat.aff12.1D
#++ Concatenating volreg and epi to anat transformations
#Script is running:
cat_matvec -ONELINE __tt_refvol.lpcregister_obla2e_mat.1D refvol.lpcregister_al_e2a_only_mat.aff12.1D -I > movvol.lpcregister_al_reg_mat.aff12.1D
#++ Applying transformation of epi to anat
#Script is running (command trimmed):
3dAllineate -base refvol.lpcregister+orig -1Dmatrix_apply movvol.lpcregister_al_reg_mat.aff12.1D -prefix movvol.lpcregister_al -input movvol.lpcregister+orig -master SOURCE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: Emperor Zhark
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./movvol.lpcregister+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:./movvol.lpcregister+orig.BRIK is 13.100002 degrees from plumb.
++ Loading datasets
*+ WARNING: base and source datasets have different handedness!
*+ WARNING: Alignment will proceed, but examine results carefully!
++ ========== Applying transformation to 1 sub-bricks ==========
++ ========== sub-brick #0 ========== [total CPU=0.1 s]
++ Output dataset ./movvol.lpcregister_al+orig.BRIK
++ total CPU time = 0.3 sec Elapsed = 0.5
++ ###########################################################
#Script is running (command trimmed):
3drefit -deoblique movvol.lpcregister_al+orig
++ 3drefit: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset movvol.lpcregister_al+orig
*+ WARNING: Over-writing dataset ./movvol.lpcregister_al+orig.HEAD
++ 3drefit processed 1 datasets
#Script is running:
rm -f AddEdge/*
#++ Applying transformation for epi to anat for @AddEdge
#Script is running (command trimmed):
3dAllineate -base refvol.lpcregister+orig -1Dmatrix_apply 'movvol.lpcregister_al_mat.aff12.1D{0}' -prefix __tt_movvol.lpcregister_alnd_rs -input __tt_movvol.lpcregister_ts_rs_ns+orig -master BASE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
++ Authored by: Emperor Zhark
** FATAL ERROR: badly formed filename: -1Dmatrix_apply 'movvol.lpcregister_al_mat.aff12.1D{0}'
#Script is running:
mkdir AddEdge
#Script is running (command trimmed):
3dcopy -overwrite __tt_refvol.lpcregister_ob+orig AddEdge/refvol.lpcregister_ns
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite __tt_movvol.lpcregister_ts_rs_ns+orig AddEdge/movvol.lpcregister_ns
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
#Script is running (command trimmed):
3dcopy -overwrite __tt_movvol.lpcregister_alnd_rs+orig AddEdge/movvol.lpcregister_al
++ 3dcopy: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
** ERROR: Can't open dataset __tt_movvol.lpcregister_alnd_rs+orig - SKIPPING
#Script is running (command trimmed):
cd AddEdge; @AddEdge refvol.lpcregister_ns+orig movvol.lpcregister_ns+orig movvol.lpcregister_al+orig; cd ..
*** Can't open dataset movvol.lpcregister_al+orig
d1: Subscript out of range.
d1: Subscript out of range.
d1: Subscript out of range.
if: Expression Syntax.
#++ Creating final output: epi data aligned to anat
# copy is not necessary
#++ Saving history
#Script is running:
3dNotes -h "align_epi_anat.py -giant_move -AddEdge -epi2anat -anat_has_skull \
no -Allineate_opts -warp shift_rotate -anat refvol.lpcregister+orig -epi \
movvol.lpcregister+orig -epi_base 0" movvol.lpcregister_al+orig
*+ WARNING: Over-writing dataset ./movvol.lpcregister_al+orig.HEAD
#++ Removing all the temporary files
#Script is running:
rm -f __tt_movvol.lpcregister*
#Script is running:
rm -f __tt_refvol.lpcregister*
# Finished alignment successfully
To view edges produced by @AddEdge, type:
cd AddEdge
afni -niml -yesplugouts &
@AddEdge
