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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 https://secure-web.cisco.com/1fMyxmsjafAHJa_lMbHaeJsspmhF-Q3odaixiH0gfbDn0gO...
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 KaneJunior Imaging Specialist
University Imaging Centers | University of Minnesota
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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 http://secure-web.cisco.com/1m6yXVH-O-LGo9G2ElxQ0d1gGwglNkj5Rk4qqeapki7eoGge... 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 https://secure-web.cisco.com/1OHV2XLqVY33enJScv_4iPydnxRIhA6JKF4c-9NUeDwf7hZ...
On Mon, May 15, 2023 at 8:50 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
External Email - Use CautionI 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 CautionHi, 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://secure-web.cisco.com/1OHV2XLqVY33enJScv_4iPydnxRIhA6JKF4c-9NUeDwf7hZ... https://secure-web.cisco.com/1fMyxmsjafAHJa_lMbHaeJsspmhF-Q3odaixiH0gfbDn0gO75B8PQS-sfrsSef_13r7kKrYi2De_3oP6ytOj0-R9bLy_EP-ALFHtYso2Jz6PaVcDqhdPJh-z2Os3HgveAxrXDirQy9Ey9Z0GcF3g6l3_mghIdsrPPzCHcZjuuSFbqUCcq-sFBB7vb8LscV2fywlCl_msjXSBqSexjzhYBI5oYSOEzzWk8c5jTokZUONGcyDqAtZD6_flHeyCLdIImqMPLVcX_8kn9JjEbNOd9K46D3C22S1dG_NsLDAJDlVXQ745e02IXXKbEUflR0lhdOINtV-B5_qfalUM-4XqQtQ/https%3A%2F%2Fmed.umn.edu%2Fuic
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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. 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://secure-web.cisco.com/1PEN_QRy7k-htNbx3a5N4QPX2gpTakY8md96cfwJWdzjmKk6... http://secure-web.cisco.com/1m6yXVH-O-LGo9G2ElxQ0d1gGwglNkj5Rk4qqeapki7eoGgehuqpRtwn89nMMH_CtaFMN9KBqW66menJG5Gb3_KyrfuzAlIrrNfBkSBYx2HwCGHHBpwmYRja6IpMWyGa39ec8j1faxtdVt8mT-7qed0H2AADXeis-blc332C4H4gtG3-GRV_alThTYlLzbfvZDIl1i2yDQ3RWPbnB0i6nr8K4yjVlhoBUjoRxFhpjXIWsilqjcqKFcgEIgrdEoqTWbJYIAQOlw6OHDGhkfR8K04176DNpCDXsjLIT9WVvvfBTXyPRbqkO9Aoo21pjwmrq/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.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 KaneJunior Imaging Specialist
University Imaging Centers | University of Minnesota
*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1BpD8bAg1tNAc9s-SeSNXb1W85cUrga4fVo8s-IfVioHA-X... https://secure-web.cisco.com/1OHV2XLqVY33enJScv_4iPydnxRIhA6JKF4c-9NUeDwf7hZbyptj5ee0NEm3Y6HXnZ0Og4LCBkWOwC-K6L7vwEABTfmSXiz_4zChEndyo8yBCJdocJ0I-IyRn5CR1JXKsTIYMHJwpn2ZuAxjRwkmyQ963gvdehiwR96EIeUGWr7_fuZ7GXKf4z9OMOtq-eeHNVNbugrrg8g6w0I1T56XXUf_XncJ8ZPG7n23Rr_D5UmCI5ebupLdDhVQNkoq4G0gR5G4r7RLCDYqObteTCYE6XOT2JrhWrdmWqCFW9ZLSNOz2wJuxXirkxrAms2Qoz0EW/https%3A%2F%2Fmed.umn.edu%2Fuic
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? 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Douglas N. Greve -
Nadia Kane