CITATION.cff

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+cff-version: 1.1.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Kashyap
+    given-names: Sriranga
+    orcid: https://orcid.org/0000-0003-0307-9773
+title: srikash/presurfer: ondu
+version: 1.0
+date-released: 2021-03-22

README.md

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-# presurfer
+# presurfer [![DOI](https://zenodo.org/badge/307506444.svg)](https://zenodo.org/badge/latestdoi/307506444)
+
+## 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')](https://github.com/srikash/3dMPRAGEise)
+<br>
+
+Optional: \
+Strip dielectric pads if used now (see [PadsOff](https://github.com/srikash/faceoff/blob/master/PadsOff), needs [ANTs](https://github.com/srikash/TheBeesKnees/wiki/Installing-Advanced-Normalization-Tools-(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