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spine-generic / data-multi-subject_DO-NOT-USE

Multi-subject data for the Spine Generic project
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manual correction of t1w and t2w images #16

Closed PaulBautin closed 4 years ago

PaulBautin commented 4 years ago

This PR contains manually corrected t1w and t2w SC segmentations for following subjects:

FILES_SEG:

FILES_GMSEG:

FILES_LABEL:

-Very little correction was applied to GMSEG because of the difficulty to localize grey matter -sub-cmrra02_T2w_RPI_r.nii.gz was not corrected because of defacing problem

Below is zipped QC report: (Second zip file contains corrections of first file for): FILES_SEG:

FILES_GMSEG:

FILES_LABEL:

qc_corr_20200729145633.zip qc_corr_20200730095951.zip

jcohenadad commented 4 years ago

@PaulBautin you need to click inside the spinal cord:

Screen Shot 2020-07-30 at 11 50 58 AM

jcohenadad commented 4 years ago

@PaulBautin i can see that some data are of very poor quality-- can you please start modality-specific issues about data quality as @valosekj did in #14?

jcohenadad commented 4 years ago

from what i see we can exclude:

jcohenadad commented 4 years ago

@PaulBautin i'm looking at both zip files, and some images appear in both zip files, which:

could you please re-upload a proper qc, without duplication? thanks

PaulBautin commented 4 years ago

I have corrected labeling, see QC: qc_corr_20200730115633.zip

Is there a reason not to allow "none type" input in a section of the config yaml file? sg_manual_correction did not allow to only do labelling corrections.

jcohenadad commented 4 years ago

I have corrected labeling, see QC: qc_corr_20200730115633.zip

the qc also contains segmentations, which is confusing

Is there a reason not to allow "none type" input in a section of the config yaml file? sg_manual_correction did not allow to only do labelling corrections.

just remove the FILES_SEG and FILES_GMSEG entries in your config file-- or you can also open an issue so we can fix it at some point

valosekj commented 4 years ago

Is there a reason not to allow "none type" input in a section of the config yaml file? sg_manual_correction did not allow to only do labelling corrections.

just remove the FILES_SEG and FILES_GMSEG entries in your config file-- or you can also open an issue so we can fix it at some point

It is probably same thing as I mentioned in this issue. I would vote for clarifying doc -- add a sentence/hint something like: "If you want to correct only labeling, include in your config yml file only FILES_LABEL key, i.e., do not include/delete FILES_SEG and FILES_GMSEG keys, and vice versa."

PaulBautin commented 4 years ago

new QC with command: sg_manual_correction -config err_file_t1w_t2w_corrected.yml -path-in data_to_correct -qc-only qc_corr_20200731105752.zip

jcohenadad commented 4 years ago

@PaulBautin can you pls remove sub-cmrra02_T2w_RPI_r.nii.gz from the manual correction, because there is the problem with the data, i.e., this should not be part of the "manual correction" PR.

jcohenadad commented 4 years ago

@PaulBautin also remove sub-sapienza04_T2star_rms.nii.gz, where the segmentation is meaningless because of poor data quality.

also: this manual corr is not complete: image

PaulBautin commented 4 years ago

DONE:

new QC: qc_corr_20200731122832.zip