Re: [Freesurfer] error message using mri_robust_template
External Email - Use Caution Hi Martin, Thank you for your email! I will try using FS 7.1.1. I have noticed that using the --inittp 0 option also gets rid of the error described. Do you think this would be an alternative ? I don't mind that it takes longer to converge. Best, Marisa Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Martin Reuter Gesendet: Freitag, 18. September 2020 13:27 An: Freesurfer support list Betreff: Re: [Freesurfer] error message using mri_robust_template 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 mailto:marisa.no...@gmail.com>> 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) (-0.959193687357,0.7102764951350742) 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] error message using mri_robust_template
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 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) > (-0.959193687357,0.7102764951350742) > > 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 > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error message using mri_robust_template
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
