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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Ricky Tong
November 29, 2005 01:36PM
Hi all,

I am just wondering if anyone have encountered any problems using @auto_tlrc when "-no_ss" flag is being used? Often times I get the warning message of

"Registration did not converge, even
without shear operation.
Check your results, the -help tips
and report persisting problems to
progam authors.

Script will stop ..."


So far I have tested 20 brains with @auto_tlrc using 3 different templates, which are TT_avg152T1+tlrc, TT_icbm452+tlrc and TT_N27+tlrc. I have absolutely no idea of which template is best for my subjects simply because this problem can occur in any of my subjects with any templates.

Say, subject 1 works with TT_avg152T1+tlrc but not the others.
subject 2 works with TT_icbm452+tlrc and TT_N27+tlrc but not TT_avg152T1+tlrc and so forth.


For example, this is the command that I used.
**********************************************
>>@auto_tlrc -no_ss -suffix _452 -base TT_icbm452+tlrc -input 3dvol+orig
**********************************************



And this is what I get.
*****************************************
Parsing ...
Using template from /haier/ricky/AFNI/linux_gcc32 ...
Padding ...
++ Program 3dZeropad: AFNI version=AFNI_2005_09_06_0927 [32-bit]
++ output dataset: ./__ats_tmp___3dvol_ref_TT_icbm452_40pad+tlrc.BRIK
Resampling ...
++ Program 3dcalc: AFNI version=AFNI_2005_09_06_0927 [32-bit]
++ Program 3dcalc: AFNI version=AFNI_2005_09_06_0927 [32-bit]
Clipping -0.000100 1042.000100 ...
++ Program 3dcalc: AFNI version=AFNI_2005_09_06_0927 [32-bit]
++ Program 3drefit: AFNI version=AFNI_2005_09_06_0927 [32-bit]
++ Processing AFNI dataset ./3dvol_rs+tlrc.HEAD
++ Changed dataset view type and filenames.
++ Program 3drefit: AFNI version=AFNI_2005_09_06_0927 [32-bit]
++ Processing AFNI dataset __ats_tmp___3dvol_resamp_NN+tlrc.HEAD
++ Changed dataset view type and filenames.
++ Program 3drefit: AFNI version=AFNI_2005_09_06_0927 [32-bit]
++ Processing AFNI dataset __ats_tmp___3dvol_resamp_edge_art+tlrc.HEAD
++ Changed dataset view type and filenames.
Registration (quintic final interpolation) ...
++ Program 3dWarpDrive: AFNI version=AFNI_2005_09_06_0927 [32-bit]
RMS[0] = 252.11 314.038 ITER = 36/137

Warning:*****************************
Registration did not converge, trying
registration without shearing.

++ THD_rename_dataset_files: rename __ats_tmp___3dvol_reg_warpdriveout+orig.HEAD -> __ats_tmp___3dvol_reg_warpdriveout_NoConvergence+orig.HEAD
++ THD_rename_dataset_files: rename __ats_tmp___3dvol_reg_warpdriveout+orig.BRIK -> __ats_tmp___3dvol_reg_warpdriveout_NoConvergence+orig.BRIK
++ Program 3dWarpDrive: AFNI version=AFNI_2005_09_06_0927 [32-bit]
RMS[0] = 252.11 314.408 ITER = 22/104

Warning:***************************
Registration did not converge, even
without shear operation.
Check your results, the -help tips
and report persisting problems to
progam authors.

Script will stop ...

********************************************************

Btw, without using the "-no_ss" flag, everything works fine. "-no_ss" means no skullstripping. But in an user's standpoint, sometimes it's important to keep the skull as well.


Thanks.

Ricky Tong

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Subject Author Posted

problem using @auto_tlrc using -no_ss flag

Ricky Tong November 29, 2005 01:36PM

Re: problem using @auto_tlrc using -no_ss flag

Godot November 29, 2005 02:25PM

Re: problem using @auto_tlrc using -no_ss flag

Ricky Tong November 29, 2005 05:12PM