Issue : isn’t SPM12 “Dartel – Run Dartel (existing templates)” implemented in nipype ?

[arianefleury]

Hi,

I’ve been trying to find the Nipype implementation for the Dartel - Run Dartel (existing templates) routine from SPM12 interface to run Dartel with my own tissue map template (TPM based on MNI and extra tissue class for tumor, see m-file at the end of this message). But I only found the spm.DARTEL() function which produces its own templates and has no input parameter for existing templates.

It seems that this specific routine isn’t implemented yet, am I right ? And if so, would it be possible to adapt the Nipype implementation of Dartel to take this case into account?

Thanks for your answer,

Ariane

SPM12 m-file for ‘Dartel – Run Dartel (Existing Templates)’:

%-----------------------------------------------------------------------
% Job saved on 18-May-2017 14:36:59 by cfg_util (rev $Rev: 6460 $)
% spm SPM - SPM12 (6906)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
matlabbatch{1}.spm.tools.dartel.warp1.images = {
{'rc1GLAS12008RM_05136012_3D_Gado.nii,1'}
{'rc2GLAS12008RM_05136012_3D_Gado.nii,1'}
}';
matlabbatch{1}.spm.tools.dartel.warp1.settings.rform = 0;
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(1).its = 3;
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(1).rparam = [1 0.5 1e-06];
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(1).K = 1;
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(1).template = {'TPMGMWM.nii'};
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(2).its = 3;
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(2).rparam = [0.5 0.25 1e-06];
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(2).K = 2;
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(2).template = {'TPMGMWM.nii'};
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(3).its = 3;
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(3).rparam = [0.25 0.125 1e-06];
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(3).K = 6;
matlabbatch{1}.spm.tools.dartel.warp1.settings.param(3).template = {'TPMGMWM.nii'};
matlabbatch{1}.spm.tools.dartel.warp1.settings.optim.lmreg = 0.01;
matlabbatch{1}.spm.tools.dartel.warp1.settings.optim.cyc = 3;
matlabbatch{1}.spm.tools.dartel.warp1.settings.optim.its = 3;

Execution environment

python 2.7.13 1 conda-forge
nipype 0.12.1 py27_1 conda-forge