Hi everybody,

I'm having problems with the alignment produced by align_anat_epi.py using an AFNI I downloaded yesterday.

I'm running the command as follows
align_epi_anat.py -anat js01.anat+orig. -epi js01.run1+orig. -epi_base 2 -child_epi js01.run?+orig.HEAD -tshift_opts "-tpattern seqplus" -AddEdge -epi2anat

I've tried both with and without the -big_move argument but to no avail.

The data I'm trying to align is from adolescents aged 14-19 in case it makes a difference.

The data comes from a Philips scanner (in NIfTI format) I use 3dcopy on these to automatically fill in the header to afni's liking.

Attached are two screen shots one showing the results with big_move and one with out it. Any ideas How I can improve the results of the alignment?

The anats are:

Dataset File: js01.anat+orig
Identifier Code: XYZ_-R6WZQrootdFFXfRPuH7-Q Creation Date: Thu Apr 9 17:04:51 2009
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 47185920 (47 million) bytes
Geometry String: "MATRIX(0.898435,-0.002038,-0.000665,-111.2928,-0.001927,-0.889867,0.123998,122.8389,0.000938,0.12378,0.891417,-45.15126):256,256,180"
Data Axes Tilt: Oblique (7.920 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -111.293 [R] -to- 117.809 [L] -step- 0.898 mm [256 voxels]
A-to-P extent: -106.263 [A] -to- 122.839 [P] -step- 0.898 mm [256 voxels]
I-to-S extent: -45.151 -to- 115.949 [S] -step- 0.900 mm [180 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '#0' datum type is float: 0 to 6906.1


and the epis are

Dataset File: js01.run1+orig
Identifier Code: XYZ_mp43FBtr2btYwHYFQ10aUQ Creation Date: Thu Apr 9 16:52:51 2009
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode: BRIK file
Storage Space: 77594624 (78 million) bytes
Geometry String: "MATRIX(3.499937,0.020903,-0.002786,-107.4734,0.020903,-3.398647,0.919511,119.6859,-0.002533,0.835919,3.738581,-2.183838):64,64,32"
Data Axes Tilt: Oblique (13.822 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -107.473 [R] -to- 113.027 [L] -step- 3.500 mm [ 64 voxels]
A-to-P extent: -100.814 [A] -to- 119.686 [P] -step- 3.500 mm [ 64 voxels]
I-to-S extent: -2.184 -to- 117.166 [S] -step- 3.850 mm [ 32 voxels]
Number of time steps = 148 Time step = 2.000s Origin = 0.000s


Bye,

Colm.