Document procedure for manually fixing SC segmentations

jcohenadad commented 2 years ago

First processing done: sct_run_batch_log.txt

Identified problematic segmentations: saved as qc_fail.yml file under the QC report.

Terminal output

```console FILES_SEG: - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P007/anat/sub-P007_UNIT1.nii.gz - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P023/anat/sub-P023_UNIT1.nii.gz - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P024/anat/sub-P024_UNIT1.nii.gz - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P014/anat/sub-P014_UNIT1.nii.gz - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P013/anat/sub-P013_UNIT1.nii.gz - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P035/anat/sub-P035_UNIT1.nii.gz - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P002/anat/sub-P002_UNIT1.nii.gz - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P005/anat/sub-P005_UNIT1.nii.gz - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P033/anat/sub-P033_UNIT1.nii.gz - /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed/sub-P034/anat/sub-P034_UNIT1.nii.gz ```

Create a new branch in the original dataset

cd ~/data.neuro/basel-mp2rage
git pull && git annex sync --no-content && git annex get .
git checkout -b jca/corrected-segs

Run:

python <PATH_TO_REPOSITORY>/preprocessing/manual_correction.py -config ~/Desktop/qc_fail.yml -path-in /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed -path-out ~/data.neuro/basel-mp2rage/

TODO:

[ ] The script does not show the axial view. @jcohenadad
[x] Add the remaining segmentations for the remaining failing subjects, including P014 and P023. Eg: if the segmentation completely failed, you can use the svm algo. Do this on another branch. @uzaymacar
[ ] Add documentation for manual correction

jcohenadad commented 2 years ago

Another pass of processing and manual correction:

Create a new branch in the original dataset

cd ~/data.neuro/basel-mp2rage
git pull && git annex sync --no-content && git annex get .
git checkout -b jca/corrected-segs-20211213

Run manual correction

python <PATH_TO_REPOSITORY>/preprocessing/manual_correction.py -config ~/Desktop/qc_fail.yml -path-in /Users/julien/temp/basel-mp2rage_20211210_120907/data_processed -path-out ~/data.neuro/basel-mp2rage/

Updated repository

51b1e51a0ff7531ebe9e9dc190065b53ba164e3d (HEAD -> master, origin/master, origin/jca/corrected-segs-20211213, origin/HEAD, jca/corrected-segs-20211213) Manual correction of sub-P0

jcohenadad commented 2 years ago

Now, we're going to create the manual segmentations for the following errored subjects:

sub-P006
sub-P004
sub-P011
sub-P017

EDIT: This has now been done and merged to master:

93110d8ebb65398dcc6e4528bf548eb7828332f1 (HEAD -> master, origin/master, origin/jca/corrected-segs-20211213-2, origin/HEAD, jca/corrected-segs-20211213-2) Added manual segmentation for sub-P017
f9d6c0fdad721d923ef8a0466f2dd3ca69024d22 Added manual segmentation for sub-P011
207c7a80b6d1bc3d4ecccee4f0918a560a8264c5 Added manual segmentation for sub-P004
518dabe79904c479441937ad4f4a3aa7741e4d01 Added manual segmentation for sub-P006

ivadomed / model_seg_ms_mp2rage