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Scripts to prepare MP2RAGE for Freesurfer

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presurfer DOI

Example

Step-0 : MPRAGEise UNI

Run presurf_MPRAGEise

MPRAGEising is better than background removal ('denoising')

Optional:
Strip dielectric pads if used now (see PadsOff, needs ANTs)

Step-1 : Get a stripMask from INV2

Run presurf_INV2

Step-2 : Get a brainMask from UNI

Run presurf_UNI

Step-3 : Freesurfer

Use the INV2 stripMask to clean up the non-brain parts of the MPRAGEised UNI image.

e.g. fslmaths MPRAGEised.nii -mul stripMask.nii MPRAGEised_stripped.nii

Run recon-all using the MPRAGEised_stripped image

Here is an example of a fully automated segmentation using presurfer + Freesurfer and laminar surfaces:


Misc. note

Run presurf_biascorrect to do just do SPM bias-correction.

Every step produces a sub-directory in the working directory containing all relevant segmentations and masks.

e.g. running presurf_INV2 creates a presurf_INV2 sub-directory

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