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This is the output I get from using mri_robust_register. It appears to have failed.
mri_robust_register --mov lab2im/brains/brain_05.nii.gz --dst atlas/atlas.nii.gz --lta affine_brain_05.lta --satit --affine
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $

--mov: Using lab2im/brains/brain_05.nii.gz as movable/source volume.
--dst: Using atlas/atlas.nii.gz as target volume.
--lta: Output transform as affine_brain_05.lta .
--satit: Will iterate with different SAT to ensure outliers below wlimit!
--affine: Enableing affine transform!

reading source 'lab2im/brains/brain_05.nii.gz'...
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
reading target 'atlas/atlas.nii.gz'...
niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented

Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
   Type Source : 3  Type Target : 3  keeping type
   Mov: (1, 1, 1)mm  and dim (528, 320, 456)
   Dst: (1, 1, 1)mm  and dim (528, 320, 456)
   Asserting both images: 1mm isotropic
    - no Mov reslice necessary
    - no Dst reslice necessary


 Registration::findSaturation
   - computing centroids
   - computing initial transform
     -- using translation info
   - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
   - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 )
   - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 4 )

   - Max Resolution used: 3
     -- gpS ( 66 , 40 , 57 )
     -- gpT ( 66 , 40 , 57 )
   - running loop to estimate saturation parameter:
     -- Iteration: 1  trying sat: 16
         min sat: 16 ( 0.269129 ), max sat: 0 ( -1 ), sat diff: -16
     -- Iteration: 2  trying sat: 32
         min sat: 16 ( 0.269129 ), max sat: 32 ( 0.14134 ), sat diff: 16
     -- Iteration: 3  trying sat: 24
         min sat: 24 ( 0.185636 ), max sat: 32 ( 0.14134 ), sat diff: 8
     -- Iteration: 4  trying sat: 28
         min sat: 28 ( 0.161066 ), max sat: 32 ( 0.14134 ), sat diff: 4
     -- Iteration: 5  trying sat: 30
         min sat: 28 ( 0.161066 ), max sat: 30 ( 0.150891 ), sat diff: 2
     -- Iteration: 6  trying sat: 29
         min sat: 28 ( 0.161066 ), max sat: 29 ( 0.156944 ), sat diff: 1
     -- Iteration: 7  trying sat: 28.5
   - final SAT: 28.5 ( it: 7 , weight check 0.158844 <= 0.16 )


 Registration::computeMultiresRegistration
   - computing centroids
   - computing initial transform
     -- using translation info
   - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 )
   - initial transform:
Ti = [ ...
 1.0000000000000                0                0 37.6192039913140
               0  1.0000000000000                0 -36.6488012913270
               0                0  1.0000000000000  0.4824356632500
               0                0                0  1.0000000000000  ]

   - initial iscale:  Ii =1

Resolution: 4  S( 33 20 28 )  T( 33 20 28 )
 Iteration(f): 1
     -- diff. to prev. transform: 30.7962
 Iteration(f): 2
     -- diff. to prev. transform: 49.8092
 Iteration(f): 3
     -- diff. to prev. transform: 91.9343
 Iteration(f): 4
     -- diff. to prev. transform: 182.169
 Iteration(f): 5
     -- diff. to prev. transform: 394.859 max it: 5 reached!

Resolution: 3  S( 66 40 57 )  T( 66 40 57 )
 Iteration(f): 1
     -- diff. to prev. transform: 571.649
 Iteration(f): 2
     -- diff. to prev. transform: 1152.35
 Iteration(f): 3
     -- diff. to prev. transform: 2382.8
 Iteration(f): 4
     -- diff. to prev. transform: 6194.58
 Iteration(f): 5
     -- diff. to prev. transform: 13876.7 max it: 5 reached!

Resolution: 2  S( 132 80 114 )  T( 132 80 114 )
 Iteration(f): 1
     -- diff. to prev. transform: 30229.2
 Iteration(f): 2
     -- diff. to prev. transform: 84881.5
 Iteration(f): 3
     -- diff. to prev. transform: 137140
 Iteration(f): 4
MyMatrix::MatrixSqrt Internal Error:
 Result too imaginary to ignore! ( 589.12 )
 Debug Info:
A = [ ...
591.7016241767593 -540.2073360700590 -0.5909768818530 -21820.2754131087277
24.1204573546435 -154.0057498115019 -0.0405379278428 3013.2761498571026
 1.9201531211277  7.6592344095763  3.3071356507170 -466.2254384688247
               0                0                0  1.0000000000000  ]

T = [ ...
573.796198605792                   -562.729608977730                    42.089766424482                   21710.111310798231                  
               0                   -136.101115799500                     9.761631095111                   -3752.029161795459                  
               0                                  0                     3.307927209682                   -122.321136673251                  
               0                                  0                                  0                     1.000000000000                    ]

U = [ ...
 -0.999444030207                     0.032777239727                    -0.006105983931                                  0                  
 -0.033122874660                    -0.997029360084                     0.069536539350                                  0                  
 -0.003808629431                     0.069700126875                     0.997560718280                                  0                  
               0                                  0                                  0                     1.000000000000                    ]

 fro( real(U * T * U^*) - A) = 2.18839e-11

Asqrt = [ ...
 24.558241482676 - 0.294201081972i -18.228379424179 + 8.877020392445i  -0.022519650376 + 0.001334138920i -967.647857472171 -241.922469141816i
  0.813893727049 - 0.396395244081i  -0.604131249234 +11.960556506402i  -0.001019678782 + 0.001797567566i  -4.809619008986 -325.957048020464i
  0.082452614585 + 0.025830574457i   0.057317845959 - 0.779393925640i   1.818704033815 - 0.000117136125i -49.088944814334 +21.240562101830i
               0                                  0                                  0                     1.000000000000                    ]

 fro( real(sqrt(A)) ^2 - A)  = 4745.28


I tried using mri_coreg, but got an issue with the licensing when I have the flags. I typed the command mri_coreg on its own and it brings up the documentation so I know it's functionality works. 

(freesurfer) kanex161@cn2008 [/scratch.global/tpengo/freesurfer/bin] % ./mri_coreg --mov lab2im/brains/brain_05.nii.gz --ref  atlas/atlas.nii.gz --reg reg.lta
SUBJECTS_DIR not defined

$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
cwd /scratch.global/tpengo/freesurfer/bin
cmdline ./mri_coreg --mov lab2im/brains/brain_05.nii.gz --ref atlas/atlas.nii.gz --reg reg.lta
sysname  Linux
hostname cn2008
machine  x86_64
user     kanex161
dof    6
nsep    2
cras0    1
ftol    0.000000
linmintol    0.001000
bf       1
bflim    30.000000
bfnsamp    30
SmoothRef 0
SatPct    99.990000
MovOOB 0
optschema 1
Seed 53
Reading in mov lab2im/brains/brain_05.nii.gz
--------------------------------------------------------------------------
ERROR: FreeSurfer license file /scratch.global/tpengo/freesurfer/.license not found.
  If you are outside the NMR-Martinos Center,
  go to MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/registration.html to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.
  A path to an alternative license file can also be
  specified with the FS_LICENSE environmental variable.

Nadia Kane                   

Junior Imaging Specialist 

University Imaging Centers | University of Minnesota

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://med.umn.edu/uic




On Mon, May 15, 2023 at 8:50 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

        External Email - Use Caution        

I don't see why not. I think the only reason it might fail is if it makes some assumptions about the voxels size. You can also try mri_coreg; I wrote this so I'm pretty sure there are no such assumptions (but robust reg might work as well)

On 5/14/2023 1:09 PM, Nadia Kane wrote:

        External Email - Use Caution        

Hi,
Can mri_robust_register be used for mouse brain atlas affine registration? What criteria need to be considered?

Thanks,
Nadia


Nadia Kane                   

Junior Imaging Specialist 

University Imaging Centers | University of Minnesota

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://med.umn.edu/uic
 



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