[△EXTERNAL]
Hi Andrew,
Sorry for the late response. I’m able to reproduce your error.
I have included Martin to the communication. He is the author of the program. He is going to take a look at
your data.
Best,
Yujing
*From:*Andrew Beaudin <abeau...@ucalgary.ca>
*Sent:* Friday, November 25, 2022 3:25 PM
*To:* Huang, Yujing <yhuan...@mgh.harvard.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
*Subject:* RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean
Error
* External Email - Use Caution *
Hi Huang,
Thank you very much for your help with this. Apologies for the delay.
You should be able to retrieve sample images from the following link (expires on Dec. 2). I have also
included a brief word document at the link that includes some details of the nifti images.
https://secure-web.cisco.com/1u-XjnB7jp5aUY3P1eL9t3mjpEr4XAP3TY2U7XxL4Sk87YBdOSl_IQZ5JxeKcPMFrkH1D-DL51W3gJTpja96AmSeeT6NQ-dEWQRnDoseAfuoXPdol4fUEj456GfCfg6j6TtlrWRZoceOKpLjcxVFnsacYsf16cLSN-f6q0Sbbc0InWMXztU4Wy6y0t1g_7ySgm0Nc6-uXHG8pXVATn179wXImzhZu1it0pGrkoYjI0g6eUpUKXmb5AwPI0oaQZUaiMUxvvZMEIDGHEmGBTYBoZBfCSn_YRcLlNDAPu9m1IlJo22qTgCbu8sgHPQszXhUWwLqcZSrhBQP4hmRgdIJumtNtYVbbc8YuFjLZXax3WT0/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ
<https://secure-web.cisco.com/1hstJ7MT7lbWknwArluI7lsJDpCaPEnPjFOntWZC705TN7hf2zZ6yi6kYZOC0uvnzY4lhzK3ZM6JenT-iUCVRXmGQD3uftAD8OYL8nRsUntQSgd62pdkysnwz7Ei0MpfFScbOiKSm0zYOh7orQWmOfvRZJYI8GvWgu9XtDcLuLHMfgMkdllTtYJdE5Ht3Rh2a17I1tqEXZCjpKzzl_Hdx6NaDHJPqGxeKLX0pSSO_LGk3WyZ7S3YL04EgD6GiMRV2KCYSn4mx2cLl7I06xdwOr9DxyUFAXoLsVoBpaUDi-KcISE065Vag1H-7HyUhCIAgQFmsEVYjvotyAmUOYZvUQw/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ>
The command call I am using is:
mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 2001A2template.lta
2001B2template.lta --average 1 --template 2001_template.nii.gz --satit
However, while troubleshooting I have also tried the following with no
success:
1) using the --iscale flag - same MyMatrix::RotationMean Error (see below for
log)
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same MyMatrix::RotationMean Error
4) using Freesurfer v7.2 - same MyMatrix::RotationMean Error
5) running mri_robust_template call on Catalina and Big Sur systems with FS v6.0 - same
MyMatrix::RotationMean Error.
Again, thank you for the help….and please let me know if your need any additional information or anything
clarified.
Andrew
----
*Andrew Beaudin, PhD* | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273
*From:*Huang, Yujing <yhuan...@mgh.harvard.edu>
*Sent:* November 22, 2022 7:32 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Cc:* Andrew Beaudin <abeau...@ucalgary.ca>
*Subject:* RE: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean
Error
[△EXTERNAL]
Hi Andrew,
Can you send us some data to debug? The link has expired. Also, the command line that you are having trouble
with.
Thanks.
Yujing
*From:*freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Andrew
Beaudin
*Sent:* Wednesday, June 29, 2022 10:45 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error
* External Email - Use Caution *
Hello Freesurfer Community,
I am trying to use mri_robust_template (with its default 6 DOF registration) outside of the Freesurfer
longitudinal pipeline to generate within-participant T1 templates from 2 time points. Unfortunately, I am
coming up against a 'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our GE 3T
Discovery 750 system, but not our colleagues' Seimens 3T Prisma images. I have pasted the output from the
--debug flag below (and attached as text file - line 188 is the MyMatrix message). If helpful, images can
be download from the following link: *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://secure-web.cisco.com/1ls7wEdSjgde9hLJaZxLUAkONj1McFRg4sysDSThCpHQydCVYcoXLchMkU6WK-Eo1berCyJLPh5WGgBga__uEASxeCDrlhfnem4jEBRSBqM4pRIEz5iCLLffWQfvSOZSAeHIAq6GAZzo8kqjl1ZMDK_HefXipddXtnNWtE55Nel7kGQp6R4aaHg3VhyLteU4C4qsGcOvda_2hwE0T0auSj6xefUzfNOBy8228vkwoarUH-lL3fyXTjsUKiICTbEOMZtoCiw5inghh0wGRL1YdJ0DpjKA2NHt7LQJnV8FqFPInmWIdEIVAQhLBcWfJaA_g4GrJramBNiQsAoDe6ItogHja9FeFwygPyC-j6Se4Rog/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ%3Fe%3DlcovfR
<https://secure-web.cisco.com/1FGQFgBoMNs00DgWtLCrKSIIdug6juLkb2Nu2KrASFJPZBjdCx_joSq08q6GYn899WbiMHITtkL3x-o5AHvRXbH-2JHAu0_Gw5aFmg9rIhsPy0Zu8zpryZYHjsE4umwwEylBRyd0TGNV3m-d5k9_IsQhRu2SYc6vj4WIaJ8F_q9uIcsgpX_QVuppEMG4lRVPp3RvveMfZRpMkehNDZJ_pJT9pje_N5viL2Zb7XZPRfaNnCKK7hTcevtyaKDqtmy85Rm2GqvtUB9vFnPFssxAMeZH7UBH2-8RQCzhCokbVocDQ7-m0q6rQ-kCKxQSNMpVdE3gMPmdjbjJ6vIqZ0RuPLkj9Labe95_FuZXUxmFfL8Y/https%3A%2F%2Fuofc-my.sharepoint.com%2F%3Af%3A%2Fg%2Fpersonal%2Fabeaudin_ucalgary_ca%2FEmL7JGE0J-BHpnRfqArO3OMBlcD4VPqRkUZKfsmKGeL2SQ%3Fe%3DlcovfR>
Briefly:
- the images are skull-stripped niftis and I am running Freesurfer 6.0
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a WSL2 Ubuntu 18.04 installation.
- the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta
2001A2template.lta 2001B2template.lta --average 1 --template 2001_template.nii.gz --satit
- I have tried the following with no success:
1) using the --iscale flag - same result as shown below.
2) using --inittp 0 - results in a 'Segmentation fault'
3) using --average 0 - same result as shown below
4) using Freesurfer v7.2 - same result as below
5) running mri_robust_template call on Catalina and Big Sur systems with FS
v6.0 - same result as below.
Currently, the only way to get mri_robust_template to work with our GE images is to run it with the
--affine flag. I would prefer to use the rigid body registration but am at a loss for why these images are
failing using the rigid body registration is failing. Any help/insights/recommendations are greatly appreciated.
Thank you very much.
Andrew
----
*Andrew Beaudin, PhD* | Postdoctoral Scholar
University of Calgary | Cumming School of Medicine
Department of Clinical Neurosciences
HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1
Phone: (403) 210-6273
DEBUG REPORT:
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
--mov: Using 2001A_T1o_brain.nii.gz as movable/source volume.
--mov: Using 2001B_T1o_brain.nii.gz as movable/source volume.
Total: 2 input volumes
--lta: Will output LTA transforms
--average: Using method 1 for template computation.
--template: Using 2001_template.nii.gz as template output volume.
--satit: Will estimate SAT iteratively!
--debug: Will output debug info and files!
reading source '2001A_T1o_brain.nii.gz'...
converting source '2001A_T1o_brain.nii.gz' to bspline ...
MRItoBSpline degree 3
reading source '2001B_T1o_brain.nii.gz'...
converting source '2001B_T1o_brain.nii.gz' to bspline ...
MRItoBSpline degree 3
Will use TP 2 as random initial target (seed 108242 ).
MultiRegistration::initializing Xforms (init 2 , maxres 0 , iterate 5 , epsit
0.01 ) :
MultiRegistration Parameters
Outdir: ./
TransOnly: false
Rigid: true
Robust: true
Satit: true
Iscale: false
IscaleOnly: false
NoMulti: false
SubsampleSize: -1
HighIt: -1
FixVoxel: false
KeepType: true
Average: 1
DoublePrec: false
BackupWeights: false
SampleType: 5
CRASCenter: false
Debug: 1
[init] ========================= TP 1 to TP 2 ==============================
Register TP 1 ( 2001A_T1o_brain.nii.gz )
to TP 2 ( 2001B_T1o_brain.nii.gz )
Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE )
Type Source : 3 Type Target : 3 keeping type
Mov: (1, 1, 1)mm and dim (176, 256, 256)
Dst: (1, 1, 1)mm and dim (176, 256, 256)
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: 3 )
- Build Gaussian Pyramid ( Limits min steps: 0 max steps: 3 )
- Max Resolution used: 2
-- gpS ( 44 , 64 , 64 )
-- gpT ( 44 , 64 , 64 )
- running loop to estimate saturation parameter:
-- Iteration: 1 trying sat: 16
min sat: 16 ( 0.729941 ), max sat: 0 ( -1 ), sat diff: -16,
(wlimit=0.16)
-- Iteration: 2 trying sat: 32
min sat: 32 ( 0.713406 ), max sat: 0 ( -1 ), sat diff: -32,
(wlimit=0.16)
-- Iteration: 3 trying sat: 64
min sat: 64 ( 0.692689 ), max sat: 0 ( -1 ), sat diff: -64,
(wlimit=0.16)
-- Iteration: 4 trying sat: 128
min sat: 128 ( 0.666858 ), max sat: 0 ( -1 ), sat diff: -128,
(wlimit=0.16)
-- Iteration: 5 trying sat: 256
min sat: 256 ( 0.637119 ), max sat: 0 ( -1 ), sat diff: -256,
(wlimit=0.16)
-- Iteration: 6 trying sat: 512
min sat: 512 ( 0.591624 ), max sat: 0 ( -1 ), sat diff: -512,
(wlimit=0.16)
-- Iteration: 7 trying sat: 1024
min sat: 1024 ( 0.550606 ), max sat: 0 ( -1 ), sat diff: -1024,
(wlimit=0.16)
-- Iteration: 8 trying sat: 2048
min sat: 2048 ( 0.485668 ), max sat: 0 ( -1 ), sat diff: -2048,
(wlimit=0.16)
-- Iteration: 9 trying sat: 4096
min sat: 4096 ( 0.370434 ), max sat: 0 ( -1 ), sat diff: -4096,
(wlimit=0.16)
-- Iteration: 10 trying sat: 8192
min sat: 8192 ( 0.19981 ), max sat: 0 ( -1 ), sat diff: -8192,
(wlimit=0.16)
-- Iteration: 11 trying sat: 16384
min sat: 8192 ( 0.19981 ), max sat: 16384 ( 0.0606314 ), sat diff:
8192, (wlimit=0.16)
-- Iteration: 12 trying sat: 12288
min sat: 8192 ( 0.19981 ), max sat: 12288 ( 0.103499 ), sat diff:
4096, (wlimit=0.16)
-- Iteration: 13 trying sat: 10240
min sat: 8192 ( 0.19981 ), max sat: 10240 ( 0.142423 ), sat diff:
2048, (wlimit=0.16)
-- Iteration: 14 trying sat: 9216
min sat: 9216 ( 0.16727 ), max sat: 10240 ( 0.142423 ), sat diff:
1024, (wlimit=0.16)
-- Iteration: 15 trying sat: 9728
min sat: 9216 ( 0.16727 ), max sat: 9728 ( 0.155264 ), sat diff: 512,
(wlimit=0.16)
-- Iteration: 16 trying sat: 9472
min sat: 9472 ( 0.160488 ), max sat: 9728 ( 0.155264 ), sat diff: 256,
(wlimit=0.16)
-- Iteration: 17 trying sat: 9600
min sat: 9472 ( 0.160488 ), max sat: 9600 ( 0.157199 ), sat diff: 128,
(wlimit=0.16)
-- Iteration: 18 trying sat: 9536
min sat: 9472 ( 0.160488 ), max sat: 9536 ( 0.159131 ), sat diff: 64,
(wlimit=0.16)
-- Iteration: 19 trying sat: 9504
min sat: 9472 ( 0.160488 ), max sat: 9504 ( 0.159604 ), sat diff: 32,
(wlimit=0.16)
-- Iteration: 20 trying sat: 9488
min sat: 9472 ( 0.160488 ), max sat: 9488 ( 0.159903 ), sat diff: 16,
(wlimit=0.16)
-- Iteration: 21 trying sat: 9480
min sat: 9480 ( 0.160034 ), max sat: 9488 ( 0.159903 ), sat diff: 8,
(wlimit=0.16)
-- Iteration: 22 trying sat: 9484
min sat: 9484 ( 0.160123 ), max sat: 9488 ( 0.159903 ), sat diff: 4,
(wlimit=0.16)
-- Iteration: 23 trying sat: 9486
min sat: 9484 ( 0.160123 ), max sat: 9486 ( 0.159831 ), sat diff: 2,
(wlimit=0.16)
-- Iteration: 24 trying sat: 9485
min sat: 9484 ( 0.160123 ), max sat: 9485 ( 0.159908 ), sat diff: 1,
(wlimit=0.16)
-- Iteration: 25 trying sat: 9484.5
- final SAT: 9485 ( it: 25 , weight check 0.159908 <= 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 -2.0251428914711
0 1.0000000000000 0 6.0311902437196
0 0 1.0000000000000 2.8105113695639
0 0 0 1.0000000000000 ]
- initial iscale: Ii =1
Resolution: 3 S( 22 32 32 ) T( 22 32 32 )
Iteration(f): 1
-- diff. to prev. transform: 2.97694
Iteration(f): 2
-- diff. to prev. transform: 0.0903233
Iteration(f): 3
-- diff. to prev. transform: 0.0191757
Iteration(f): 4
-- diff. to prev. transform: 0.0116139
Iteration(f): 5
-- diff. to prev. transform: 0.00140989 <= 0.01 :-)
Resolution: 2 S( 44 64 64 ) T( 44 64 64 )
Iteration(f): 1
-- diff. to prev. transform: 1.81202
Iteration(f): 2
-- diff. to prev. transform: 0.199033
Iteration(f): 3
-- diff. to prev. transform: 0.00925469 <= 0.01 :-)
Resolution: 1 S( 88 128 128 ) T( 88 128 128 )
Iteration(f): 1
-- diff. to prev. transform: 1.02247
Iteration(f): 2
-- diff. to prev. transform: 0.0229168
Iteration(f): 3
-- diff. to prev. transform: 0.000719712 <= 0.01 :-)
Resolution: 0 S( 176 256 256 ) T( 176 256 256 )
Iteration(f): 1
-- diff. to prev. transform: 0.664624
Iteration(f): 2
-- diff. to prev. transform: 0.0108463
Iteration(f): 3
-- diff. to prev. transform: 0.000585613 <= 0.01 :-)
- final transform:
Tf = [ ...
0.9994709868827 -0.0113151175724 -0.0304912199489 4.8530791096303
0.0126622658755 0.9989355014916 0.0443568583483 2.1370162587100
0.0299568590234 -0.0447194809223 0.9985503265352 5.4716006804225
0 0 0 1.0000000000000 ]
- final iscale: If = 1
CentroidT = [ 86.5860705940972 104.6067830299094 138.6676688710562
1.0000000000000 ]
CentroidSinT = [ 88.1595712077722 107.7558909090270 139.3780739549505
1.0000000000000 ]
Centroid = [ 87.3728209009347 106.1813369694682 139.0228714130033
1.0000000000000 ]
MyMatrix::RotationMean input(s) not rotation
meant = [ -1.2248131651588 1.2892456671960 3.1420193014715 ]
Input rotation's max deviation from rotation is: 0.000393411
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