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Did you see the part where it says:
WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented
You probably need to set the qform or the sform
On 5/15/2023 11:35 AM, Nadia Kane wrote:
External Email - Use Caution
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_coregon 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.
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get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
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Nadia Kane
Junior Imaging Specialist
University Imaging Centers | University of Minnesota
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On Mon, May 15, 2023 at 8:50 AM Douglas N. Greve
<dgr...@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
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