Hi Marisa, the main goal of robust_template is to remove rigid motion between scans. So the first question is, do you really need (want) affine? The next question is, if this still occurs in FS 7.1.1 I remember dimly that I worked on this some years ago (basically allow a larger threshold, as it was too tight and numerical instabilities often triggered this, when it was totally fine to continue). So try that first and let me know.
Best, Martin > On 16. Sep 2020, at 10:27, Marisa Nordt <[email protected]> wrote: > > > > 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) > (-0.1111959193687357,0.7102764951350742) > > 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 > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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