Hello AFNI team,
When removing obliquity from my original images (just converted DICOM to Nifti) using the command:
3drefit -overwrite -deoblique dset_anat_deob
for anatomical images (deobliquing the anatomical images before @animal_warper was advised in a previous post)
and
3drefit -overwrite -deoblique dset_func_deob
for functional images
Originally (before deoblique) dset_func_deob and dset_anat_deob were perfectly aligned (despite that they had different oblique)
After deoblique dset_func_deob appeared shifted when compared to dset_anat_deob.
3Dinfo before deoblique
Anat:
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 25,165,824 (25 million) bytes
Geometry String: "MATRIX(0.499882,0,0.010845,-63.49814,-0.004364,0.45773,0.201158,-33.41661,-0.009928,-0.201205,0.457622,-22.09527):256,256,192"
Data Axes Tilt: Oblique (23.760 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -63.498 [R] -to- 64.002 [L] -step- 0.500 mm [256 voxels]
A-to-P extent: -33.417 [A] -to- 94.083 [P] -step- 0.500 mm [256 voxels]
I-to-S extent: -22.095 -to- 73.405 [S] -step- 0.500 mm [192 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is short: 0 to 1586
Func:
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 262,144 (262 thousand) bytes
Geometry String: "MATRIX(1.991842,0,0.180458,-64.53218,-0.064086,1.869635,0.70736,-17.80025,-0.168695,-0.710257,1.862009,-6.530476):64,64,32"
Data Axes Tilt: Oblique (21.408 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -64.532 [R] -to- 61.468 [L] -step- 2.000 mm [ 64 voxels]
A-to-P extent: -17.800 [A] -to- 108.200 [P] -step- 2.000 mm [ 64 voxels]
I-to-S extent: -6.530 -to- 55.470 [S] -step- 2.000 mm [ 32 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is short: 0 to 28215
3Dinfo after deoblique
Anat:
Template Space: ORIG
Dataset Type: Anat Bucket (-abuc)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 25,165,824 (25 million) bytes
Geometry String: "MATRIX(0.5,0,0,-63.49814,0,0.5,0,-33.41661,0,0,0.5,-22.09527):256,256,192"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -63.498 [R] -to- 64.002 [L] -step- 0.500 mm [256 voxels]
A-to-P extent: -33.417 [A] -to- 94.083 [P] -step- 0.500 mm [256 voxels]
I-to-S extent: -22.095 -to- 73.405 [S] -step- 0.500 mm [192 voxels]
Number of values stored at each pixel = 1
-- At sub-brick #0 '?' datum type is short: 0 to 889
Func:
Template Space: ORIG
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 183,500,800 (184 million) bytes
Geometry String: "MATRIX(2,0,0,-64.53218,0,2,0,-17.80025,0,0,2,-6.530476):64,64,32"
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Anterior-to-Posterior
third (z) = Inferior-to-Superior [-orient RAI]
R-to-L extent: -64.532 [R] -to- 61.468 [L] -step- 2.000 mm [ 64 voxels]
A-to-P extent: -17.800 [A] -to- 108.200 [P] -step- 2.000 mm [ 64 voxels]
I-to-S extent: -6.530 -to- 55.470 [S] -step- 2.000 mm [ 32 voxels]
Number of time steps = 700 Time step = 0.70000s Origin = 0.00000s Number time-offset slices = 32 Thickness = 2.000
-- At sub-brick #0 '?' datum type is short: 0 to 17639
-- At sub-brick #1 '?' datum type is short: 0 to 17319
-- At sub-brick #2 '?' datum type is short: 0 to 18897
** For info on all 700 sub-bricks, use '3dinfo -verb' **
What can I do to have dset_func_deob aligned to dset_anat_deob after deoblique?
Clem
