Dear Riki,

> The MRI (MPRAGE) is taken after the grid implantation to identify  
> the location of electrordes (as a signal void due to property of  
> platinum electrode) for epilepsy patients having invasive evaluations.
>
> I would like to coregister the brain with subdural electrodes (i.e.,  
> partially distorted because of the implantation) to the brain before  
> the electrode implantation (non-distorted brain of the same  
> patient). Attached, please see an example (MRI taken after grid  
> implantation).
> In the majority of cases the following configuration parameters do  
> well, but in some it did not work well.
>
> While FLIRT using bet'ed MRI did a relatively good job, FNIRT  
> ocassionally locally enlarge/warp the lateral parietal area more  
> than we expected (cortex enlarged out of the lateral parietal  
> surface of MPRAGE taken before the implantation).
>
> For configuration files for FNIRT, we used T1_2_MNI152_2mm.conf  
> (default config file of FNIRT) except
> --in=MPRAGEwithGrid.nii.gz
> --ref=MPRAGEbeforeGrid.nii.gz
> --inmask=skull stripped MPRAGEwithGrid.nii.gz
> --refmask=skull stripped MPRAGEbeforeGrid
>
> I used --inmask and --refmask because the MRI after grid  
> implantation usually has locall swelling outside the brain (some  
> fuid collection epidurally or in the scalp).

It sounds like you have done most of the things I would recommend. The  
critical thing is that fnirt assumes that everything that is present  
in one image is present also in the other (though it may have a  
different size and shape). So e.g. if it finds a ventricle in one  
brain it expects to find one in the other as well.

This assumption is of course not fulfilled when you have a pathology  
(e.g. a tumor) or some foreign object (electrode) in one of the images  
and not in the other. Our recommendation then is to mask these areas  
out using some suitable combination of --inmask and --refmask. And it  
sounds like you have already done that.

Another possibility (which does not address your electrodes, but might  
help those intensity hot-spots) is to use a higher resolution for the  
bias-field. It will mean longer execution time, and may not work if it  
means that intensity and shape gets too strongly correlated. But it  
would be worth a try.

Another thing you might try is to complement your data with a list of  
point correspondences. This is a hidden feature, that is quite  
untested, that might potentially help you. If you are able to manually  
identify unique points in both volumes you can put these in two text  
files, and that means that these points will serve as an anchor  
between the two volumes (and might prevent fnirt from doing silly  
things in that region).

Let us say e.g. that you have managed to identify two points on the  
cortical surface in both volumes. You should then create a file with  
the points identified in the --ref file, e.g.

ref_pl.txt contains
15 45 67
18 52 63

and one for the --in file
in_pl.txt contains
20 42 56
23 50 50

when running fnirt you then specify these with

fnirt --ref=....      .....  --refpointlist=ref_pl.txt -- 
inpointlist=in_pl.txt

These points are not "completely anchored", but rather have some  
slack. The amount of slack is given by the

--pointlistlambda

parameter. The default is --pointlistlambda=1 , but you may wish to  
experiment with it.

Also, please note that there is a reason I hid this option for the  
release. I need to do lots more testing of it, and there is a risk you  
may encounter problems with it.

Good luck Jesper