AFNI Message Board

History of AFNI updates  

|
November 12, 2021 01:12PM
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
Subject Author Posted

3drefit -deoblique

Doughboys November 12, 2021 01:12PM

Re: 3drefit -deoblique

Doughboys November 12, 2021 02:45PM

Re: 3drefit -deoblique

ptaylor November 12, 2021 02:54PM

Re: 3drefit -deoblique

Doughboys November 12, 2021 03:24PM

Re: 3drefit -deoblique

ptaylor November 12, 2021 03:50PM

Re: 3drefit -deoblique

Doughboys November 12, 2021 04:53PM

Re: 3drefit -deoblique

ptaylor November 12, 2021 05:18PM

Re: 3drefit -deoblique

Doughboys November 12, 2021 05:25PM

Re: 3drefit -deoblique

ptaylor November 12, 2021 05:36PM

Re: 3drefit -deoblique

Doughboys November 22, 2021 04:09PM

Re: 3drefit -deoblique

Daniel Glen November 22, 2021 04:23PM

Re: 3drefit -deoblique

Doughboys November 24, 2021 01:27PM

Re: 3drefit -deoblique

ptaylor November 24, 2021 04:14PM

Re: 3drefit -deoblique

Doughboys November 24, 2021 04:35PM

Re: 3drefit -deoblique

ptaylor November 24, 2021 05:19PM

Re: 3drefit -deoblique

ptaylor November 24, 2021 09:22PM

Re: 3drefit -deoblique

Doughboys November 25, 2021 11:44AM

Re: 3drefit -deoblique

ptaylor November 26, 2021 09:42AM

Re: 3drefit -deoblique

Doughboys November 26, 2021 02:00PM

Re: 3drefit -deoblique

Doughboys November 29, 2021 11:31AM

Re: 3drefit -deoblique

Doughboys November 29, 2021 03:14PM

Re: 3drefit -deoblique

Doughboys November 29, 2021 04:11PM



Sorry, only registered users may post in this forum.

Click here to login