Hello,
Hopefully someone can help me with the following questions. Currently I am working on a group of TBI (traumatic Brain Injury) patients. Since some of them have a focal lesion, I would like to use a lesion mask in order to normalize the brains properly to the standard brain.
I already created my lesion masks and would like to perform FNIRT on those patients. I know now that I can run FEAT normally and that I can re-run FNIRT on the command line using the lesion mask, and then updating my feat/reg directory. I hope I am doing this correctly. I am however wondering what to do with the B0 unwarping. I have a fieldmap of these patients, and I would like to use these in my analyses as I did in my healthy controls. So, if I use updatefeatreg after I have run FNIRT on the command line, does it still have the information of the B0 unwarping?
This is the command line that I run:
fnirt --ref=MNI152_T1_2mm.nii.gz --in=t1_brain.nii.gz --inmask=mylesionweights.nii.gz --iout=fnirted_T1_brain.nii.gz --config=T1_2_MNI152_2mm.cnf --aff=highres2standard.mat
Another question related to this issue: In some cases the FNIRT registration with lesion mask does not work properly at all. In those specific cases I would like to use FLIRT instead of FNIRT. I noticed however that a similar strategy as for the FNIRT method is not possible. You will get another output and the updatefeatreg command does not work. So, I have tried this through the FLIRT gui, using the lesion mask as a weighting volume. I can then run FEAT normally (with the output data of the FLIRT analyses as the input data), and I should deselect the registration options. But, again I have a problem with the Fieldmap here. I cannot unselect all registration options if I select the B0 unpwarping.
So, actually the main thing that I would like to know is whether I am doing things correctly, and whether I can combine lesion masks with fieldmaps (B0 unwarping) in both FNIRT and FLIRT.
Thank you very much for your help!
Peter
|