Adding the python script for manual labeling #2
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(I'd rather have a PR to discuss the code ) |
This add the -path option to manual labeling which give the root of Bids path This changes the output of get_bids_sub to remove the BIDS root path
sop.md
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| python manual-labeling/manual_labeling.py -file list_todo_update.txt -author lucas -path Path_to_duke/ \[-correct 1 -o label_tmp\] | ||
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| - -file: txt file that contains the list of all images inside bids root folder that you want to process separated by '\n'.The format in sub-xx/anat/sub-xxx_xxx.nii.gz. Can be obtained with get_bids_sub.py. | ||
| - -path : Path th Bids root folder (duke) with a '/' at the end |
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Minor comment: You can check / adjust for missing / I think
sop.md
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| - -path : Path th Bids root folder (duke) with a '/' at the end | ||
| - -author: Author name that will appear on the .json file | ||
| - -correct: Boolean. default is 0. If correct is 1, the script will look for existing label and open them with the -ilabel option from sct_label_utils so you can verify/correct existing label. | ||
| - -o: in the output folder given by the 5th argument, you will find in BIDS convention sub-xxx/anat/sub-xxx_labels-disc-manual.nii.gz and sub-xxx/anat/sub-xxx_lables-disc-manual.json" if this is empty this will save under BIDS_PATH/derivatives/labels/sub-xx/anat/xxx |
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I would recommend to remove "by the 5th argument".
| to end : performa keyboard interrupt from the terminal (ctrl+c). This will update the list by deleting the viewed subjects. don't forget to commit and push it on github. | ||
| Specific: | ||
| possible file suffix to file are _acq-sag_T2w, _T2w, _T1w, _acq-sagcerv_T2w | ||
| suffix to label is labels-disc-manual |
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Would it be relevant to add a parameter that controls this suffix?
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it's actually a remain of a first version where I asked for file suffix. I'll remove it from the SOP. Now there are no reason that I can think of. we can add a case for the constraint on it if you think this could be useful.
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I was simply thinking: if one day we want to label pmj instead of the disc --> pmj-manual instead of labels-disc-manual.
But we can leave it as it is for now :-)
get_BIDS_sub.py
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| required=True, | ||
| help="path to BIDS Data", | ||
| ) | ||
| mandatoryArguments.add_argument( |
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constraint, ope, value are great.
Possible avenue of improvement: add possibility to have multiple constraints (separated by commas?).
Could also use a config file to specify those.
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Is there a reason for requiring them as mandatory? I would recommend to change for optional.
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Not really, in my mind there was another solution to get all file but I just realized that's will not work with the 'manual labeling.py' script. (ls > file.txt would get you all the subject but not image file) will fix
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Comment about the optional argument in get_ids_sub fixed in d8343ee |
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I have run --> Will correct the code to discard |
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I tried to following command and it worked well! After doing Ctrl+C, it updated the list.txt --> great! |
Co-authored-by: alexfoias <[email protected]>
Co-authored-by: alexfoias <[email protected]>
What about adding minimal resolution? something like pixdim <= 1 |
lrouhier
changed the title
This PR adds the python script. It is here for discussion.
Added
Manual_labeling.py :this script takes as arguments the list of image file you want to look at, the author name, and acorrectflag.If the flag is used: this will run sct_label_utils with the -ilabel option and open the existing file for the user to check/correct. If not used the script will skip files that are already labeled.