Hi, Rick.

I tried align_epi_anat.py with the following command line structure:

nice align_epi_anat.py -partial_coverage -anat 1808.anat+orig -epi 1808.3Dout.Lum01+orig -suffix al2anat -epi_base 0 -volreg off -tshift off -epi2anat -child_epi Uniform_Lum+orig

and get the following error:

#++ align_epi_anat version: 1.01
#++ turning off volume registration
#++ epi_base set
#++ -child_epi option given
#++ Found child epi /apu/home/qrmano/From_old_apu_home2/pub/VWFA_1_study/wf.1808/Concat_Session1and2/Uniform_Lum+orig
#++ Removing all the temporary files
#Script is running:
rm -f __tt_1808.3Dout.Lum01*
#Script is running:
rm -f __tt_1808.anat*
#Script is running (command trimmed):
3dcopy 1808.anat+orig __tt_1808.anat+orig
++ 3dcopy: AFNI version=AFNI_2008_02_01_1144 (Apr 15 2008) [32-bit]
#++ Removing skull from anatomical data
#Script is running (command trimmed):
3dSkullStrip -input __tt_1808.anat+orig -prefix __tt_1808.anat_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_1808.anat+orig -b __tt_1808.anat_ns+orig -expr 'a*step(b)' \
-prefix __tt_1808.anat_ns_orig_vol
to generate a new masked version of the input.
#Script is running (command trimmed):
3dbucket -prefix __tt_1808.3Dout.Lum01_tsal2anat 1808.3Dout.Lum01+orig'[0]'
++ 3dbucket: AFNI version=AFNI_2008_02_01_1144 (Apr 15 2008) [32-bit]
#++ resampling epi to match anatomical data
#Script is running (command trimmed):
3dresample -master __tt_1808.anat_ns+orig -prefix __tt_1808.3Dout.Lum01_tsal2anat_rsal2anat -inset __tt_1808.3Dout.Lum01_tsal2anat+orig -rmode Cu
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dSkullStrip -input __tt_1808.3Dout.Lum01_tsal2anat_rsal2anat+orig -prefix __tt_1808.3Dout.Lum01_tsal2anat_rsal2anat_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_1808.3Dout.Lum01_tsal2anat_rsal2anat+orig -b __tt_1808.3Dout.Lum01_tsal2anat_rsal2anat_ns+orig -expr 'a*step(b)' \
-prefix __tt_1808.3Dout.Lum01_tsal2anat_rsal2anat_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_1808.3Dout.Lum01_tsal2anat_rsal2anat_ns+orig
#++ Applying threshold of 3238.000000 on /apu/home/qrmano/From_old_apu_home2/pub/VWFA_1_study/wf.1808/Concat_Session1and2/__tt_1808.3Dout.Lum01_tsal2anat_rsal2anat_ns+orig
#Script is running (command trimmed):
3dcalc -datum float -prefix __tt_1808.3Dout.Lum01_tsal2anat_rsal2anat_ns_wtal2anat -a __tt_1808.3Dout.Lum01_tsal2anat_rsal2anat_ns+orig -expr 'min(1,(a/3238.000000))'
++ 3dcalc: AFNI version=AFNI_2008_02_01_1144 (Apr 15 2008) [32-bit]
++ Authored by: A cast of thousands
#++ Aligning anatomical data to epi data
#Script is running (command trimmed):
3dAllineate -lpc -wtprefix __tt_1808.anat_nsal2anat_wtal -weight __tt_1808.3Dout.Lum01_tsal2anat_rsal2anat_ns_wtal2anat+orig -source __tt_1808.anat_ns+orig -source_automask+4 -prefix __tt_1808.anat_nsal2anat -base __tt_1808.3Dout.Lum01_tsal2anat_rsal2anat_ns+orig -cmass+xy -1Dmatrix_save 1808.anatal2anat_mat.aff12.1D -weight_frac 1.0 -maxrot 6 -maxshf 10 -VERB -warp aff -master SOURCE
++ 3dAllineate: AFNI version=AFNI_2008_02_01_1144 (Apr 15 2008) [32-bit]
++ Authored by: Emperor Zhark
++ Loading datasets
++ 1964871 voxels in -source_automask+4
++ Zero-pad: not needed
++ 907113 voxels [10.2%] in weight mask
++ Output dataset ./__tt_1808.anat_nsal2anat_wtal+orig.BRIK
++ Number of points for matching = 907113
++ Local correlation: blok type = 'RHDD(6.54321)'
++ center of mass shifts = 1.2 -11.2 0.0
++ shift param auto-range: -65.3..67.7 -77.7..55.3 -43.3..43.3
+ Range param#4 [z-angle] = -6.000000 .. 6.000000
+ Range param#5 [x-angle] = -6.000000 .. 6.000000
+ Range param#6 [y-angle] = -6.000000 .. 6.000000
+ Range param#1 [x-shift] = -8.830647 .. 11.169353
+ Range param#2 [y-shift] = -21.217831 .. -1.217830
+ Range param#3 [z-shift] = -10.000000 .. 10.000000
+ 12 free parameters
++ Normalized convergence radius = 0.001000
++ ======= Allineation of 1 sub-bricks using Local Pearson Correlation Signed =======
++ Memory usage now = 106988726 (107 million): about to start alignment loop
++ ========== sub-brick #0 ==========
++ Start coarse pass
+ * Enter alignment setup routine
+ - copying base image
+ - copying source image
+ - Smoothing base; radius=11.11
+ - Smoothing source; radius=11.11
+ - copying weight image
+ - using 666 points from base image
+ * Exit alignment setup routine
+ - Search for coarse starting parameters
+ 412 total points stored in 5 'RHDD(12.8945)' bloks
+ - Scanning 95:*.*.....*.....*.*...*.........
+ - best random kval:
0 v=-4.43996: 4.50 -4.55 -3.33 4.00 4.00 2.00
1 v=-4.25529: 3.84 -2.46 -6.30 3.77 1.61 2.61
2 v=-4.18312: -1.50 -2.46 -6.30 -3.77 1.61 -2.61
3 v=-4.04269: 3.14 -3.47 -9.05 3.58 3.51 0.58
4 v=-3.9761: 5.87 -2.04 -7.50 1.75 2.29 4.28
5 v=-3.94936: 4.50 -4.55 3.33 4.00 -4.00 4.00
6 v=-3.93726: -1.50 -2.46 -6.30 -3.77 1.61 2.61
7 v=-3.91719: -2.16 -4.55 -3.33 -4.00 4.00 -4.00
8 v=-3.89626: 4.50 -4.55 3.33 2.00 -4.00 4.00
9 v=-3.86514: -0.80 -3.47 -9.05 -3.58 3.51 0.58
10 v=-3.82319: -2.16 -4.55 -6.67 -4.00 4.00 -2.00
11 v=-3.80723: 4.50 -4.55 -3.33 4.00 4.00 4.00
12 v=-3.79567: 4.50 -4.55 -3.33 2.00 4.00 4.00
13 v=-3.79271: -2.16 -4.55 -3.33 -4.00 2.00 -2.00
14 v=-3.78629: -2.16 -4.55 -3.33 -4.00 2.00 -4.00
+ - optimized random kval:
0 -5.33561: 3.87 -1.22 -4.66 4.10 4.76 1.36
1 -5.23718: 3.04 -1.52 -5.23 2.48 2.26 3.54
2 -5.90206: -1.05 -1.22 -3.30 -3.78 2.34 -2.67
3 -4.57577: 2.01 -2.88 -7.55 3.08 5.28 0.90
4 -5.34483: 3.77 -1.22 -4.77 2.04 2.67 5.17
5 -5.40944: 4.39 -1.22 0.59 3.55 -3.52 4.09
6 -4.99264: 0.20 -1.22 -5.52 -2.77 1.94 2.73
* 7 -5.95751: -2.18 -1.23 -4.75 -4.52 4.74 -4.68
8 -5.41338: 3.07 -1.23 0.74 1.01 -4.01 3.13
9 -5.68758: -0.40 -1.27 -4.86 -4.37 4.86 -0.29
10 -5.88195: -1.67 -1.22 -4.31 -4.79 3.85 -3.21
11 -5.349: 4.08 -1.29 -3.94 2.56 3.69 3.50
12 -5.39995: 4.48 -1.22 -4.50 2.70 4.64 4.49
13 -5.85615: -0.46 -1.22 -3.11 -3.55 2.15 -1.36
14 -5.93455: -2.19 -1.22 -2.96 -4.17 1.97 -5.45
+ - save #14 in trials
+ - save #2 in trials
+ - save #10 in trials
+ - save #13 in trials
+ - save #9 in trials
+ - save #8 in trials
+ - Search CPU time = 1.6 s
++ Start refinement #1 on 4 coarse parameter sets
+ * Enter alignment setup routine
+ - Smoothing base; radius=5.07
+ - Smoothing source; radius=5.07
+ - retaining old weight image
+ * Exit alignment setup routine
+ 498 total points stored in 12 'RHDD(8.28028)' bloks
+ - param set #1 has cost=-2.878990
+ - param set #2 has cost=-2.779612
+ - param set #3 has cost=-2.980349
+ - param set #4 has cost=-3.182678
++ Start refinement #2 on 4 coarse parameter sets
+ * Enter alignment setup routine
+ - Smoothing base; radius=2.32
+ - Smoothing source; radius=2.32
+ - retaining old weight image
+ * Exit alignment setup routine
+ 466 total points stored in 11 'RHDD(6.94149)' bloks
+ - param set #1 has cost=-1.693273
+ - param set #2 has cost=-2.032570
+ - param set #3 has cost=-1.705179
+ - param set #4 has cost=-1.883466
+ - Total refinement CPU time = 15.3 s; 3481 funcs
++ Fine pass begins
+ * Enter alignment setup routine
+ - retaining old weight image
+ - using 907113 points from base image
+ * Exit alignment setup routine
+ 814794 total points stored in 1023 'RHDD(6.54321)' bloks
+ - cost(#1)=-0.075917 *
+ - cost(#2)=-0.086390 *
+ - cost(#3)=-0.264675 *
+ - cost(#4)=-0.010828
+ - cost(#5)=-0.017851
+ - Initial fine Parameters = 0.3408 -1.2221 -1.3587 -0.4490 0.8227 -1.2273 0.9864 1.0341 0.9538 -0.0305 0.0264 0.0041
+ - Initial cost = -0.264675
+ - Finalish cost = -0.488907 ; 284 funcs
+ - Final cost = -0.507445 ; 435 funcs
+ Final fine fit Parameters = 1.3526 -1.2179 -2.3409 -0.7311 1.5173 -0.2705 1.0030 1.0051 1.0012 0.0023 0.0241 -0.0188
+ - Fine CPU time = 274.5 s
++ Computing output image
++ image warp: parameters = 1.3526 -1.2179 -2.3409 -0.7311 1.5173 -0.2705 1.0030 1.0051 1.0012 0.0023 0.0241 -0.0188
++ Memory usage now = 279918398 (280 million): end of sub-brick alignment
++ Memory usage now = 57095074 (57 million): end of sub-brick loop (after cleanup)
++ Output dataset ./__tt_1808.anat_nsal2anat+orig.BRIK
++ Memory usage now = 39270271 (39 million): after writing output dataset
++ Wrote -1Dmatrix_save 1808.anatal2anat_mat.aff12.1D
++ total CPU time = 373.5 sec
++ Memory usage now = 3300643 (3.3 million): end of program (after final cleanup)
++ ###########################################################
#++ Aligning /apu/home/qrmano/From_old_apu_home2/pub/VWFA_1_study/wf.1808/Concat_Session1and2/1808.3Dout.Lum01+orig to anat
#++ Inverting anat to epi matrix
#Script is running:
cat_matvec -ONELINE 1808.anatal2anat_mat.aff12.1D -I >& 1808.3Dout.Lum01al2anat_mat.aff12.1D
Syntax error: Bad fd number
#++ Applying transformation of epi to anat
#Script is running (command trimmed):
3dAllineate -base __tt_1808.anat_ns+orig -1Dmatrix_apply 1808.3Dout.Lum01al2anat_mat.aff12.1D -prefix 1808.3Dout.Lum01al2anat -input 1808.3Dout.Lum01+orig -VERB -warp aff
++ 3dAllineate: AFNI version=AFNI_2008_02_01_1144 (Apr 15 2008) [32-bit]
++ Authored by: Emperor Zhark
** FATAL ERROR: Can't read -1Dmatrix_apply '1808.3Dout.Lum01al2anat_mat.aff12.1D'
#**ERROR Could not apply transformation to epi data
** ERROR - script failed

Any ideas?

Thanks,

Tino