presurfer

Example

Step-0 : MPRAGEise UNI

Run presurf_MPRAGEise <br>

<img src="https://github.com/srikash/TheBeesKnees/blob/main/imgs/presurfer_step0.gif" width="400">

MPRAGEising is better than background removal ('denoising') <br>

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

<img src="https://github.com/srikash/TheBeesKnees/blob/main/imgs/presurfer_step0b.gif" width="400">

Step-1 : Get a stripMask from INV2

Run presurf_INV2 <br>

<img src="https://github.com/srikash/TheBeesKnees/blob/main/imgs/presurf_INV2_output.png" width="400">

Step-2 : Get a brainMask from UNI

Run presurf_UNI <br>

<img src="https://github.com/srikash/TheBeesKnees/blob/main/imgs/presurf_UNI_output.png" width="400">

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 <br>

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

<img src="https://github.com/srikash/TheBeesKnees/blob/main/imgs/freesurfer_seg.png" width="1200"> <br> <img src="https://github.com/srikash/TheBeesKnees/blob/main/imgs/drake_presurfer.jpg" width="400">

Misc. note

Run presurf_biascorrect to do just do SPM bias-correction. <br>

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

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