Dear FSL experts,
Sorry for asking this question a third time - there has been no answer to two previous versions of this email on this list and we have just found no solutions to our problems so far which is why your input would be extremely helpful for us:
We have a bunch of DTI-datasets from patients who have undergone functional hemispherectomy. Since we want to run voxelwise analyses, we need to normalize these highly deformed brains. It seems that the normalization of T1 is affected by a field bias (i.e. occipital hyperintensities and frontal hypointensities). We, therefore, want to correct the field bias. There are four quesions we have:
question1. When we generate a bias field by means of FAST, it turns out to be affected by the low signal in the lesioned hemisphere. Now we wonder whether we can run FAST with the lesion masked out?
question2. Is it possible to create some kind of average field-map out of several unlesioned-brains (who have been scanned with the same sequence and the same scanner) bias-fields (generated by means of FAST) and apply this on the lesioned ones?
question3. Should we use segmentation with FAST to remove the CSF before creating the bias field?
question4. Is there any advantage in using mfast (e.g. with a T2) while creating this bias-field (if the bias field is only noticeable on the T1)?
Any help on this is highly appreciated.
Thank you so much!!!
Best,
Theodor.
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