Adding the python script for manual labeling #2

lrouhier · 2020-05-15T20:49:53Z

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 a correct flag.
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.
Script to list all sagittal images --> use get_BIDS_sub.py -i PATH_TO_BIDS -constraint orientation -value RPI -ofile OUTPUT_NAME.
SOP for manual labeling of intervertebral disc

lrouhier · 2020-05-15T20:50:26Z

(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

charleygros · 2020-05-27T01:19:52Z

sop.md

+python manual-labeling/manual_labeling.py -file list_todo_update.txt -author lucas -path Path_to_duke/ \[-correct 1 -o label_tmp\]
+
+- -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


Minor comment: You can check / adjust for missing / I think

charleygros · 2020-05-27T01:20:53Z

sop.md

+- -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


I would recommend to remove "by the 5th argument".

charleygros · 2020-05-27T01:22:42Z

sop.md

+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


Would it be relevant to add a parameter that controls this suffix?

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.

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 :-)

charleygros · 2020-05-27T01:25:25Z

get_BIDS_sub.py

+        required=True,
+        help="path to BIDS Data",
+    )
+    mandatoryArguments.add_argument(


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.

Is there a reason for requiring them as mandatory? I would recommend to change for optional.

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

lrouhier · 2020-05-27T02:38:05Z

Comment about the optional argument in get_ids_sub fixed in d8343ee

charleygros · 2020-05-27T03:43:11Z

I have run get_BIDS_path.py on a small dataset where some processed files where stored and got:

sub-05/anat/sub-05_T1w.nii.gz
sub-05/anat/label_c2c3_T2w.nii.gz
sub-05/anat/warp_curve2straight.nii.gz
sub-05/anat/sub-05_T2w_seg.nii.gz
sub-05/anat/warp_straight2curve.nii.gz

--> Will correct the code to discard warp files. Minor

charleygros · 2020-05-27T03:54:55Z

I tried to following command and it worked well!

python manual_labeling.py -file list-generated.txt -author charley -path ~/data/spineGeneric/barcelona/

After doing Ctrl+C, it updated the list.txt --> great!

alexfoias

@lrouhier I tried the script and it worked well, I added some suggestion otherwise is good.

If there a way of excluding some images for which the labeling would be hard to mark. For example this one:

get_BIDS_sub.py

manual_labeling.py

Co-authored-by: alexfoias <[email protected]>

lrouhier · 2020-05-27T18:30:55Z

@lrouhier I tried the script and it worked well, I added some suggestion otherwise is good.

If there a way of excluding some images for which the labeling would be hard to mark. For example this one:

What about adding minimal resolution? something like pixdim <= 1

lrouhier added 2 commits May 15, 2020 16:37

first version of the script (WIP)

67235b4

Modified with an option to skip existing label

599d771

lrouhier and others added 14 commits May 19, 2020 16:49

scrpit that retrieve BIDS file

e9495d4

correction of output file name

c799481

error on list name

6fab4c6

added output folder (if not same as input)

265eae4

added something for best view

de47052

some files had more than 15 discs

273a798

Modification for task sharing.

59ff681

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

adding sop

805f350

added image

4617a4f

added auto update of the list with made subject

59c915d

modified sop for stoping

70c45d5

modification for -file argument

57f7186

modification for output change

b33396a

sop: minor fixes

8c0a765

charleygros reviewed May 27, 2020

View reviewed changes

modification for no condition

d8343ee

better looking sop (Charley comment)

6cb3ba5

charleygros added 3 commits May 27, 2020 13:44

get_BIDS_sub: robust to not provided arg

78442f4

get_BIDS_sub: get only sub-*.nii.gz

755bece

sop.md: typo

f7f67da

charleygros approved these changes May 27, 2020

View reviewed changes

alexfoias reviewed May 27, 2020

View reviewed changes

get_BIDS_sub.py Outdated Show resolved Hide resolved

manual_labeling.py Outdated Show resolved Hide resolved

lrouhier and others added 2 commits May 27, 2020 14:28

Update get_BIDS_sub.py (help issue)

fb9d37e

Co-authored-by: alexfoias <[email protected]>

Update manual_labeling.py (typo missing letter)

cb64694

Co-authored-by: alexfoias <[email protected]>

added minimal resolution

5a0d685

lrouhier changed the title ~~(WIP) Adding the python script for manual labeling~~ Adding the python script for manual labeling May 27, 2020

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Adding the python script for manual labeling #2

Adding the python script for manual labeling #2

lrouhier commented May 15, 2020 •

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Adding the python script for manual labeling #2

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