registering anatomical images for grids/dimensions that do not match

maitra · January 27, 2021, 5:24pm

Hi,

I have a set of 12 structurals images (T1-weighted being the first one) and I am trying to get them registered to a template. The template file is called mni_template.nii.gz and the 12 structurals are in ZHRTS1.nii.gz.

I tried the following:


3dvolreg -twopass -twodup -heptic -clipit -rotcom -verbose -verbose -prefix S3.2nd.REG -base 'ZHRTS1.nii.gz[0]' mni_template.nii.gz

++ 3dvolreg: AFNI version=AFNI_20.2.08 (Jul 31 2020) [64-bit]
++ Authored by: RW Cox
++ Notice: -clipit is now the default
++ Reading in base dataset /home/maitra/Datasets/sMRI/MR-TIM/ZHRTS1.nii.gz
** AFNI converts NIFTI_datatype=4 (INT16) in file /home/maitra/Datasets/sMRI/MR-TIM/mni_template.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.
++ centers of base and input datasets are 41.23 mm apart
** Input /home/maitra/Datasets/sMRI/MR-TIM/mni_template.nii.gz and base /home/maitra/Datasets/sMRI/MR-TIM/ZHRTS1.nii.gz don't have same dimensions!
   Input: nx=121  ny=161  nz=201
   Base:  nx=256  ny=256  nz=20
** Input /home/maitra/Datasets/sMRI/MR-TIM/mni_template.nii.gz and base /home/maitra/Datasets/sMRI/MR-TIM/ZHRTS1.nii.gz don't have same grid spacing!
   Input: dx=-1.500  dy=-1.500  dz= 1.500
   Base:  dx= 0.938  dy= 0.938  dz= 6.000
** Input /home/maitra/Datasets/sMRI/MR-TIM/mni_template.nii.gz and base /home/maitra/Datasets/sMRI/MR-TIM/ZHRTS1.nii.gz don't have same orientation!
   Input: L-R P-A I-S
   Base:  R-L A-P I-S 
** FATAL ERROR: perhaps you could make your datasets match?

I have never done this before, and I am not sure how to fix these problems and would benefit from some advice.

Here is my 3dinfo out put for the files:


$ 3dinfo -verb ZHRTS1.nii.gz 
++ 3dinfo: AFNI version=AFNI_20.2.08 (Jul 31 2020) [64-bit]

Dataset File:    /home/maitra/Datasets/sMRI/MR-TIM/ZHRTS1.nii.gz
Identifier Code: XYZ_UWykEadDCDmcefW0kQ_7jg  Creation Date: Thu Mar 28 21:36:43 2019
Template Space:  ORIG
Dataset Type:    Echo Planar (-epan)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   31,457,280 (31 million) bytes
Geometry String: "MATRIX(0.9375,0,0,-119.5312,0,0.9375,0,-119.5312,0,0,6,-57):256,256,20"
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:  -119.531 [R] -to-   119.531 [L] -step-     0.938 mm [256 voxels]
A-to-P extent:  -119.531 [A] -to-   119.531 [P] -step-     0.938 mm [256 voxels]
I-to-S extent:   -57.000 [I] -to-    57.000 [S] -step-     6.000 mm [ 20 voxels]
Number of time steps = 12  Time step = 4000.00000ms  Origin = 0.00000ms  Number time-offset slices = 20  Thickness = 6.000
  -- At sub-brick #0 '#0' datum type is short:            0 to           237
  -- At sub-brick #1 '#1' datum type is short:            0 to           217
  -- At sub-brick #2 '#2' datum type is short:            0 to           202
  -- At sub-brick #3 '#3' datum type is short:            0 to           285
  -- At sub-brick #4 '#4' datum type is short:            0 to           181
  -- At sub-brick #5 '#5' datum type is short:            0 to           184
  -- At sub-brick #6 '#6' datum type is short:            0 to           318
  -- At sub-brick #7 '#7' datum type is short:            0 to           179
  -- At sub-brick #8 '#8' datum type is short:            0 to           160
  -- At sub-brick #9 '#9' datum type is short:            0 to           327
  -- At sub-brick #10 '#10' datum type is short:            0 to           191
  -- At sub-brick #11 '#11' datum type is short:            0 to           173

----- HISTORY -----
[rpg@groucho.umm.edu: Wed Feb 20 11:06:39 2002] to3d -session Results -xFOV 120R-L -yFOV 120A-P -zFOV 60I-S -prefix TS1 -epan -time:zt 20 12 4000 alt+z '3D:0:0:256:256:20:func_1/ana.*.img'
[sroys@groucho.umm.edu: Tue Mar 12 16:04:06 2002] 3dvolreg -prefix ZHRTS1 -zpad 4 -base 5 -heptic -dfile ZHRTS1+orig.reg -clipit TS1+orig.BRIK


$ 3dinfo -verb mni_template.nii.gz 
++ 3dinfo: AFNI version=AFNI_20.2.08 (Jul 31 2020) [64-bit]
** AFNI converts NIFTI_datatype=4 (INT16) in file /home/maitra/Datasets/sMRI/MR-TIM/mni_template.nii.gz to FLOAT32
     Warnings of this type will be muted for this session.
     Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none.

Dataset File:    /home/maitra/Datasets/sMRI/MR-TIM/mni_template.nii.gz
Identifier Code: NII_F1sXB5JMA0w5SfIJOoqeoQ  Creation Date: Wed Jan 27 11:22:20 2021
Template Space:  TLRC
Dataset Type:    Anat Bucket (-abuc)
Byte Order:      LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode:    NIFTI
Storage Space:   15,662,724 (16 million) bytes
Geometry String: "MATRIX(-1.5,0,0,90,0,-1.5,0,130,0,0,1.5,-190):121,161,201"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Left-to-Right
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient LPI]
R-to-L extent:   -90.000 [R] -to-    90.000 [L] -step-     1.500 mm [121 voxels]
A-to-P extent:  -110.000 [A] -to-   130.000 [P] -step-     1.500 mm [161 voxels]
I-to-S extent:  -190.000 [I] -to-   110.000 [S] -step-     1.500 mm [201 voxels]
Number of values stored at each pixel = 1
  -- At sub-brick #0 '?' datum type is float

I am happy to load the data somewhere if it helps in providing better context.

Many thanks in advance for any help/suggestions and best wishes,
Ranjan

maitra · January 27, 2021, 7:03pm

I wanted to also add that I tried using the following:


align_epi_anat.py -anat mni_template.nii.gz -epi ZHRTS1.nii.gz -epi_base 0 -master_epi mni_template.nii.gz -epi2anat -giant_move

And it sort of works, however, the FOV for the mni_template.nii is larger than the one for the ZHRTS1 image volumes so it is not clear to me how to get the FOVs to match.

All I am wanting to do is to align the 12 image volumes in ZHRTS1.nii.gz to mni_template.nii.gz according to registration of the first volume in ZHRTS1.nii.gz to mni_template.nii.gz (within the same FOV).

Thanks again!
Ranjan

dglen · January 27, 2021, 10:31pm

You can use @SSwarper for each of your structural input datasets using
-base ~/abin/MNI152_2009_template_SSW.nii.gz for your template.