Lesion segmentation protocol

lesion_segmentation_protocol.md

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+# Lesion segmentation protocol
+
+The following details the protocol for Multiple Sclerosis (MS) lesion segmentation in the spinal cord.
+Imaging the spinal cord is often essential to confirm the diagnosis of MS. That is because the lesions of the spinal cord are included in the McDonald diagnostic criteria, which considers dissemination in space and in time [(Thompson et al. 2018)](https://pubmed.ncbi.nlm.nih.gov/29275977/). While the MAGNIMS-CMSC-NAIMS working group recommends to use at least two sagittal images for MS diagnosis, still, axial imaging is mentioned as optional in international imaging guidelines [(Wattjes et al. 2021)](https://pubmed.ncbi.nlm.nih.gov/34139157/).
+For detecting MS lesions in the spinal cord, two main contrasts emerge: PSIR and STIR contrasts. New studies [(Peters et al. 2024)](https://pubmed.ncbi.nlm.nih.gov/38289376/)[(Fechner et al. 2019)](https://pubmed.ncbi.nlm.nih.gov/30679225/) showed that using PSIR contrasts improved MS lesion detection in the spinal cord. [(Fechner et al. 2019)](https://pubmed.ncbi.nlm.nih.gov/30679225/) showed that the PSIR contrast showed a higher signal-to-noise (SNR) ratio compared to the STIR contrast. 
+
+## Criteria to segment MS lesions in the spinal cord:
+
+- Do not segment lesions in images with too many artifacts (such as this [example](https://github.com/ivadomed/canproco/issues/53#issue-1938136790)). Preferably, add the image to the exclude file so that it isn’t used for model training…
+- When segmenting lesions on thick slices, always look at the adjacent slices, as partial volume effect can sometimes reduce the appearance of a lesion (close to noise level).
+- Unless otherwise stated, do not segment lesions above the first vertebrae (because here we focus only on MS lesions in the spinal cord). 
+- For lesions segmentations which you are not 100% sure, flag the subject and report it for external validation of the segmentation.
+
+## How to manually segment lesions
+
+- MS spinal cord lesions can either (i) be automatically segmented from an algorithm and then manually corrected, or (ii) manually segmented from scratch. In the former case, make sure to use the JSON file that was created by the automatic segmentation algorithm, in order to track provenance:
+
+```json
+{
+        "GeneratedBy": [
+            {
+                "Name": "2D nnUNet model model_ms_seg_sc-lesion_regionBased.zip",
+                "Version": "https://github.com/ivadomed/canproco/releases/tag/r20240125",
+                "Date": "2024-01-26"
+            }
+        ]
+    }
+```
+
+- To manually create/correct the segmentation, please use the manual-correction (https://github.com/spinalcordtoolbox/manual-correction) repository. The command can be inspired from this: 
+
+```console
+python manual_correction.py -path-img ~/data/canproco -config ~/config_seg.yml  -path-label ~/data/canproco/derivatives/labels  -suffix-files-lesion _lesion-manual -fsleyes-dr="-40,70"
+``` 
+
+- A Quality Control (QC) report should be produced using SCT, and added to a GitHub issue for further validation by other investigators. Using SCT, you can review lesion segmentation in the axial or sagittal plane:
+
+```console
+sct_qc -i {image_file} -d {lesion_seg_file} -s {sc_seg_file} -p sct_deepseg_lesion -plane {sagittal, axial} -qc {canproco_qc_folder}
+```  
+
+- If you are not sure about the segmentation on a subject, it should be flagged on GitHub for a more open discussion: here are some examples [(1)](https://github.com/ivadomed/ms-lesion-agnostic/issues/4#issuecomment-1947326493) and [(2)](https://github.com/ivadomed/ms-lesion-agnostic/issues/4#issuecomment-1947338624)
+
+## Step 1: Get familiar with FSLeyes and SCT:
+It is common practice to use FSLeyes at NeuroPoly for visual inspection of MRI images and manual segmentation of MS lesions. Therefore, naturally, the first step of the lesion segmentation process is to complete the FSLeyes tutorial ([FSLeyes documentation](https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/userdoc/) and [video tutorial](https://www.youtube.com/playlist?list=PLIQIswOrUH69qFMNg8KYkEGkvCNEwlnfT)). Trainees are encouraged to learn keyboard shortcuts (ctrl+F to toggle an image, shift+↑ to scroll through volumes, ...).
+
+Furthermore, it is recommended to get familiar with SCT for creating QCs and for manual correction ([SCT tutorial](https://spinalcordtoolbox.com/user_section/tutorials.html)). 
+
+## Step 2: Spinal cord anatomy and lesion segmentation
+Before, moving on to MS lesion segmentation, trainees are advised to study the neuroanatomical structures of healthy spinal cords. Trainees should look at healthy spinal cords in MRI images of different contrasts: T2w, T1w, PSIR, STIR, MP2RAGE... A public dataset will be built for this purpose.
+
+To learn the specificity of MS lesions, trainees should work on differentiating MS lesions from Spinal Cord Injury (traumatic and non-traumatic) and DCM. A training dataset will be built especially for this case (TO DISCUSS: BUILDING A (PUBLIC) REPO TO TRAIN TO DISTINGUISH PATHOLOGIES). 
+
+One of the most challenging task of MS lesion segmentation is to distinguish the border of a lesion and the cerebrospinal fluid (CSF). To learn where to draw the lesion border, a set of tricky examples validated by a NeuroRadioligist will be created. (TO DISCUSS AS WELL). 
+
+Finally, for trainees will little or no experience with MS lesion segmentation, a checklist will be built to avoid being overwhelmed by the multiple images/contrasts/acquisitions. We typically recommend to start with the view in the highest resolution (often the sagittal view) to first identify lesions, and to move to other contrast/acquisition to validate the segmentation borders and lesion detection. During this step, playing with the brightness and the contrast is key. After locating the lesion to be traced, we recommend starting in a middle slice around the middle of the lesion and then move toward each end of the lesioned area. We also recommended frequently scrolling back and forth around the slice they are tracing on to ensure border consistency.
+
+## Taxonomy to evaluation lesion segmentation
+The following section details the different types of errors which occur during lesion segmentation. It is based on the condensed Nascimento Taxonomy:
+
+<img width="522" alt="nascimento_taxonomy" src="https://github.com/ivadomed/canproco/assets/67429280/36d9e45e-4a36-40f0-a4f5-e5f3ea3f06a0">
+
+## Sources
+This lesion segmentation protocol was inspired from these ressources: 
+- deSouza NM, van der Lugt A, Deroose CM, et al. Standardised lesion segmentation for imaging biomarker quantitation: a consensus recommendation from ESR and EORTC. Insights Imaging. 2022;13(1):159. Published 2022 Oct 4. doi:10.1186/s13244-022-01287-4 : [link](https://pubmed.ncbi.nlm.nih.gov/36194301/)
+- Lo BP, Donnelly MR, Barisano G, Liew SL. A standardized protocol for manually segmenting stroke lesions on high-resolution T1-weighted MR images. Front Neuroimaging. 2023;1:1098604. Published 2023 Jan 10. doi:10.3389/fnimg.2022.1098604 : [link](https://pubmed.ncbi.nlm.nih.gov/37555152/)
+