Re: [Freesurfer] starting longitudinal pipeline after mri_robust_template

[Marisa Nordt]

External Email - Use Caution

Hi Martin,

Thank you for your email! What is the best way to stop the long pipeline
after a certain step in a way that allows continuing from there?

Best,
Marisa

Am Do., 22. Okt. 2020 um 11:54 Uhr schrieb Martin Reuter <
mreu...@mgh.harvard.edu>:

> Hi Marisa,
>
> That should be possible.
> You can run the long pipeline up to that step, replace the corresponding
> files with your version and continue from there.
>
> Best, Martin
>
> On 1. Oct 2020, at 10:32, Marisa Johanna Nordt 
> wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I have a question regarding the longitudinal pipeline: Is it possible to
> start the longitudinal pipeline after a template (using
> mri_robust_template) has already been created in a separate step?
>
> Thank you so much,
>
> Marisa
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[Freesurfer] error message using mri_robust_template

[Marisa Nordt]

External Email - Use Caution

Hello,



I am using mri_robust_template with the ‘--affine’ option to create
individual templates (using freesurfer version
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). For each
timepoint I use that timepoint's T1.mgz as the input. For some subjects
this works well. However, for others I am receiving an error message (*
WARNING: TP 3 to 1 did not converge !!  MatrixLog Error: Result too
imaginary to ignore). I am attaching the full command and the error message
below.

Do you have thoughts on how to trouble-shoot this issue? I have looked
at the input
files and these seem to be ok.

Thank you!

Best,

Marisa



mri_robust_template --template template.nii.gz --affine --satit \

--mov Tp1T1.mgz Tp2T1.mgz Tp3T1.mgz \

--lta Tp1totemplate.lta Tp2totemplate.lta Tp3totemplate.lta \

--mapmov Tp1totemplate.nii.gz Tp2totemplate.nii.gz Tp3totemplate.nii.gz





- running loop to estimate saturation parameter:

* WARNING: TP 3 to 1 did not converge !!



 MatrixLog Error:

  Result too imaginary to ignore! ( 6.23199e-16 )

 A = 1.006576323240725 0.003084002656233406 -0.03645397216347104

-0.006991580325416484 1.011866325424678 -0.05229335553407307

0.03777040431253831 0.04392492645068569 1.002740736902102



 T = (1.00563233346774,0.0606675705194677)
(0.001071185761943805,0.00660486005552916)
(0.006657281419514499,0.004121077514717164)

(0,0) (1.009918718632024,-3.183217578417441e-16)
(-0.001219644877272269,-0.006241389920134279)

(0,0) (0,0) (1.00563233346774,-0.06066757051946813)



 U = (0.06522427283350557,-0.4086418628970923)
(-0.4512115300813958,-0.6429736578063935)
(0.4435972821778756,0.1223605486029275)

(0.1324402433691656,-0.5811769288411271)
(0.396861124383305,0.4645450375452963)
(0.5209342533284942,0.004429342327522456)

(-0.6671781011025059,-0.1682972455202441)
(-0.001010631409214958,0.09844371568609764)
(-0.959193687357,0.7102764951350742)



 fro( real(U * T * U^*) - A) = 1.736855929375805e-15



 log(A) = (0.007247004124560403,-2.550043509685906e-16)
(0.003840124735798771,3.469446951953614e-17)
(-0.03616149457717018,1.07552855510562e-16)

(-0.00594730233232413,1.249000902703301e-16)
(0.0129351237191556,-2.289834988289385e-16)
(-0.05197693653405921,5.334274688628682e-17)

(0.03770072871406291,-2.432949675057472e-16)
(0.0434964642601452,7.199102425303749e-17)
(0.004553620359034822,-2.775557561562891e-16)



 fro( exp(real(log(A))) - A)  = 1.311226128713136e-15
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