[△EXTERNAL]
Hi Andrew,
I have added an option ‘--frobnorm-thresh <>’ to mri_robust_template in Freesurfer dev branch. It can be
used to set threshold for MyMatrix::RotationMean(). The default is 0.0001.
Increasing the threshold didn’t help when I tested it with your data. The change is not in release version
yet.
Best,
Yujing
*From:*Andrew Beaudin <abeau...@ucalgary.ca>
*Sent:* Monday, February 6, 2023 7:25 PM
*To:* Huang, Yujing <yhuan...@mgh.harvard.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
*Cc:* Reuter, Martin,Ph.D. <mreu...@mgh.harvard.edu>
*Subject:* RE: [Freesurfer] mri_robust_template - MyMatrix::RotationMean Error
* External Email - Use Caution *
Hi Huang and Martin,
Apologies for the delay in replying to your email. Thank you very much for looking into this issue. I am
finally getting back to these analyses as we have more follow-up data.
I have tried using bias corrected skull-stripped images with the settings recommended (-iscale and -sat 5
(and tried 8)), but with no luck. The work around with mri_robust_register and then mri_concat (with
–median) flag works, but regarding the last point, what threshold are you referring to and how do I change
it? Is it a flag in the mri_robust_template call?
The point I am referring to is:
“- Finally, in robust_template I also get the error about deviation from rotation. For some reason, that I
could not yet find out, the first registration of A to B is not perfectly a rigid transform (some small
deviation from a rotation matrix, maybe very subtle shearing as the determinant is still very close to 1, so
no scaling). This could be a numerical issue. Anyway increasing the threshold to 0.001 should fix this. Or
did you get another error after that for this specific case?”
Thanks again.
Andrew
----
*Andrew Beaudin, PhD* | Research Associate
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:* December 21, 2022 8:45 AM
*To:* Andrew Beaudin <abeau...@ucalgary.ca>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
*Cc:* Reuter, Martin,Ph.D. <mreu...@mgh.harvard.edu>
*Subject:* RE: [Freesurfer] mri_robust_template - MyMatrix::RotationMean Error
[△EXTERNAL]
Hi Andrew,
Sorry for the late response. Copied below is the suggestions from Martin.
“
I looked at those images. A few points:
- bias fields seem to be very different, I think using --iscale helps a little here, if very high accuracy
of the registration is important, one should do a bias field removal beforehand.
- manually setting the sat to anything between 5 and 8 also looked like it
helps --sat 5 in robust register
- robust register can be used if only two time points are involved to register into a mid space using
—halfdst halfmov and halfdstlta outputs you get those images and transforms. Only thing missing is the
actual template image which for two time points is simply the average of the two images after alignment in
the mid space (so probably mri_calc or some other tool can compute that average image if it is needed).
- Scalp is changing a lot here across time, not sure why. How far are these time points apart? What type of
data (aging, disease, treatment) is this? There are also noticeable changes in the brain. Anyway, best
results are when using the skull stripped images, it is also faster. In freesurfer we work with norm.mgz in
the longitudinal pipeline which are both skull stripped an bias corrected.
- Finally, in robust_template I also get the error about deviation from rotation. For some reason, that I
could not yet find out, the first registration of A to B is not perfectly a rigid transform (some small
deviation from a rotation matrix, maybe very subtle shearing as the determinant is still very close to 1, so
no scaling). This could be a numerical issue. Anyway increasing the threshold to 0.001 should fix this. Or
did you get another error after that for this specific case?
“
*From:*Andrew Beaudin <abeau...@ucalgary.ca>
*Sent:* Wednesday, December 7, 2022 1:30 PM
*To:* Huang, Yujing <yhuan...@mgh.harvard.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
*Cc:* Reuter, Martin,Ph.D. <mreu...@mgh.harvard.edu>
*Subject:* Re: [Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean
Error
* External Email - Use Caution *
Hi Yujing,
No problem at all. I really appreciate yours, and now Martin's, help with this issue. If you would like
to start with dicoms, please let me know.
Again, thank you both for your help.
Andrew
----
*Andrew Beaudin, PhD* | Research Associate
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 [mailto:yhuan...@mgh.harvard.edu
<mailto:yhuan...@mgh.harvard.edu>]
*Sent:*Wednesday, December 7, 2022 at 10:27
*To:*Andrew Beaudin <abeau...@ucalgary.ca> <mailto:abeau...@ucalgary.ca>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
*Cc:*Reuter, Martin,Ph.D. <mreu...@mgh.harvard.edu>
<mailto:mreu...@mgh.harvard.edu>
*Subject:*[Freesurfer] Fwd: mri_robust_template - MyMatrix::RotationMean Error
[△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> <mailto:abeau...@ucalgary.ca>
*Sent:* Friday, November 25, 2022 3:25 PM
*To:* Huang, Yujing <yhuan...@mgh.harvard.edu>
<mailto:yhuan...@mgh.harvard.edu>; Freesurfer support
list <freesurfer@nmr.mgh.harvard.edu>
<mailto: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/18_TETxNr15d9aD22XzTUgdrwGkccp3G_kOPTWfaokkAvkwzC07hk_ScRWVFe43tZvvs2RkMb9PR1Pw-0MtcmEvj1r6oUDeWVsNneeH0deZ5SwQvrDhyEGCEKNBc1X1yqtInzUe23lQ9RuGlWQGlDkyuHHb_9h_5Voy87JrxmxRNxmfQrJB1LrHDaDWsHZnifbhOVQMqilICmFvJHe1H4EJUFwmta8sZjUpmLq8u5OBB9Q5sqT9pf_5M5ue7CmdAN1E1gztYXlz6_jzoF3kBnUjfZUsY472d4mkKlQDG4CmSLL1t9T00gCwIfgZgoIuxkNAw_MtTu8zSxLwV2mAJuycS_IzByCwlp-lfruj1q3sA/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/1VAax-tZHitSCWUqdBMUuPeuN2cvOLRXL1Iy-Cvlt-nre0opFt9yzff6BIfitq_0mfVKvuNZyvfjnq4Q7RK2L6XZb1W3TIA7SdnE7g4yn4VhUAlnxrTSWh-P3ngk472Qqv0zGDdxTLmMiBL1mOjV9AeDPgLwlLwkcd1nc7FiGCQeOQkVPyPXOJxTt6jrgw5T_7pr7ov98JXw-HnGIqC4hW_xCo-0w13s_MUUKGH4Dzh8zsvNsZzPDLVB5O-L1e4LcFJGcb3n9DCrXqucw4zegUh1FWhgswSGERaa7RhRLd-XV_H1ktgPxo3wDpKl7cIFvMXZ73x-_14WJ2CV5mRhyJtFUWTO7r7JcTMy07uYhWGo/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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