ANTs SyN normalization

[Vinny]

Hi,
I applied the latest update to lead-DBS and for some reason the ANTs SyN normalization no longer works i.e., after a few diagnostic runs, my computer freezes; ANTs SyN normalization had worked before I had applied the update.
I tried the SPM12 DARTEL nonlinear normalization and that appears to work fine.
Thanks for your help!
Vinny

[ningfei]

Hi Vinny,

I guess it’s memory problem. Your computer froze because it’s swapping due to limited memory. We updated ANTs parameters (hopefully improve the precision) in the latest release. ANTs SyN itself is very memory demanding, especially if you use ANTs SyN + Subcortical Refine. So better to run it on a machine with large RAM. ANTs SyN + Subcortical Refine can take 20-30GB memory. ANTs SyN may also take 10+GB memory.
In the development version of lead, we preset some ANTs parameter sets with some other settings in the setting window, from which you can choose the SyN Quick one if you want to do a quick test with ANTs and your system has limited memory.

Best,
Ningfei

[Vinny]

Hi Ningfei,
I had suspected a memory issue as well but wanted to make sure since ANTs SyN had worked on my laptop prior to the update. How do I access the development version of lead? Do I have to modify the ea_prefs file? Thank you very much for your help,

Kind regards,
Vinit

[andreashorn]

Hi Vinny,

yes, the update brought some changes to ANTs that take up too much memory. We already identified this as a problem and have incorporated some presets where users can choose a preset that also works well on laptops.
You can install the development version by following the steps highlighted in “Install via Github” in the manual (see Help/Support>Manual above). Or simply wait a bit until we release a new version soon.

Sorry for the inconvenience.

Best, Andy

[Vinny]

Hi Andy,

Not a problem and thanks for your help. I’ll try on my lab computer with a larger RAM but will also wait for the new version to be released. The normalization is pretty good with the SPM12 DARTEL nonlinear procedure though.

Kind regards,
Vinny

[Vinny]

Hi,
I had applied the latest update, ie, today, and ran ANTs normalization for the nonlinear registration step. Please note the following error message. Thanks.
Vinny

Error using eval
Undefined function or variable ‘ea_antspreset_SyN_default’.
Error in ea_ants_nonlinear (line 84)
apref=eval(funname);
Error in ea_normalize_ants (line 79)
ea_ants_nonlinear(to,from,[directory,options.prefs.gprenii],weights,options,options.prefs.machine.normsettings.ants_scrf);
Error in ea_autocoord (line 94)
eval([options.normalize.method,'(options)’]); % triggers the normalization
function and passes the options struct to it.
Error in ea_run (line 95)
ea_autocoord(options);
Error in lead_dbs>run_button_Callback (line 201)
ea_run(‘run’,options);
Error in gui_mainfcn (line 95)
feval(varargin{:});
Error in lead_dbs (line 43)
gui_mainfcn(gui_State, varargin{:});
Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_dbs(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

[andreashorn]

Hi Vinny,

sorry for that!
It’s easy to fix, you only need to click on the Settings button next to the ANTs normalization name (the popup menu where you choose the normalization routine) once and choose a setting. Then it should work.
The default name changed and we forgot to update that. Thanks for letting us know!

Best, Andy

[ningfei]

Hi Vinny,

This issue has been just fixed. You can also try to “Apply Hofix” from lead dbs “Install” menu.

Best,
Ningfei

[Vinny]

Thanks Andy and Ningfei, it works great!

Best,
Vinny

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