Dear SPMers,

I have some questions about the integration of VBM8 toolbox with DARTEL. I hope these are easy short-answer questions...

I'm running an analysis using VBM8 with the following parameters

"Estimation options"
     Tissue Probability Map:     *spm8\toolbox\Seg\TPM.nii

Question: This TPM is only used to remove non-brain tissue from the image, right?

"Extended options"
     Spatial normalization:     High-dimensional: Dartel

Question: This option uses *spm8\toolbox\vbm8\Template_6_IXI550_MNI152.nii as template, which is in MNI space, right?

"Writing options"
     Grey matter (the same for WM and CSF)
          Native space:     yes

Question: the *_seg8.mat file contains the parameters of the segmentation, so I could segment another scan of the same subject using this file?

Question: The native space GM segment p1*.nii is registered with the *spm8\toolbox\vbm8\Template_6_IXI550_MNI152.nii, in MNI space, right? Are these still probabilities of each voxel to be GM (or WM or CSF)?

Question: The *_seg8.txt contains the volumes of GM, WM and CSF. Are these the number of voxels in each segment multiplied by the voxel size or the sum of all "voxel value x voxel size" (accounting for voxels with probability values < 1) ?

"Writing options"
     Deformation fields: forward + inverse

Question: Do these fields map from the individual to the template, in this case the *spm8\toolbox\vbm8\Template_6_IXI550_MNI152.nii? If I want to know the volume of a certain structure (say the left Thalamus for example), I would warp a mask of the left Thalamus (from marsbaar-aal for example, after exporting it to the space of *spm8\toolbox\vbm8\Template_6_IXI550_MNI152.nii) to the individual using the inverse deformation field? And on which image should I calculate the volume (native GM 'p1*.nii', normalized GM 'wrp1*.nii', modulated normalized GM 'm0wrp1*.nii' ?)? Now, once again, is it sufficient to count the number of voxels of the "individual mask" and multiply by the original voxel size or should I get the values of each voxel in the GM segment, multiply by voxel size and sum all of them up?

After running "VBM8: Estimate & Write" I run the module "Run DARTEL (create Templates)", using rp1*_affine.nii, the GM segments after an affine registration to the MNI template (as I chose high-dimensional normalization, is this the *spm8\toolbox\vbm8\Template_6_IXI550_MNI152.nii template?).
This creates a flow field for each subejct: 'u_rp1*_affine_DARTEL_template_name.nii', which I then use to 'Run DARTEL (create Warped)', with modulation, and get a modulated GM segment of each subject, in the space of the group-DARTEL-template.

Question: What are the ends (group-DARTEL-template to individual?) of these flow field mappings? Can these flow fields be used to compute volumes of structures? How can I do these and on which images (modulated DARTEL warped GM 'mwrp1*_affine.nii', native GM 'p1*.nii', DARTEL exported 'rp1*_affine.nii' ?) should I do it?

Question: The Marsbar ROIs were not created in my group-DARTEL-template but in MNI space. Is this a problem? Should I use the default VBM8 deformation fields and segment images or can I use the DARTEL flow fields and warped segments to calculate volumes of structures?

Sorry for the long e-mail. I hope you can help me.

Many thanks in advance.

Regards,

João Duarte