Train model with new datasets

jcohenadad commented 1 year ago

[x] Add new data (@jcohenadad)
[x] Curate data (name file properly according to BIDS, move files to derivatives, etc.) (@kiristern)
[x] Check segmentations (@mchen1110 )
[x] Train new model (@jcohenadad) see https://github.com/ivadomed/model_seg_ms_mp2rage/issues/58

jcohenadad commented 1 year ago

I copied the new MP2RAGE dataset under duke:mri/basel/INsIDER_SCT_Segmentations_COR. @kiristern as we discussed would you mind BIDSifying these data and putting them somewhere temporary (eg: duke:temp/kiri) and then I will review and put it in our git-annex data server. Few things:

could you confirm you have read access to the data on duke?
there are scripts that Alex used to BIDSify the data (you don't have to start from scratch): here: data.neuro.polymtl.ca:/datasets/basel-mp2rage/scripts
Importantly: some of the patients overlap with what is in data.neuro.polymtl.ca:/datasets/basel-mp2rage so we should make sure to not duplicate subjects. I think these are the first 35 patients (starts with "P", and controls are "C") but this needs to be verified.
I notice that there is only one segmentation file for these updated data, while there are two segmentation files for the 35 patients we already have. I'll ask who did the segmentations so we can mention this in the JSON metadata file
On that note: the current dataset of 35 patients has in fact 3 segmentation files. The 3rd is labeled under my name. @uzaymacar do you remember how it was generated? is this 3rd segmentation the majority voting of the first 2? Or is that a 'curated' segmentation revised by me?

kiristern commented 1 year ago

@jcohenadad sorry for the delay. I just checked and I don't have access to duke/mri

jcohenadad commented 1 year ago

@jcohenadad sorry for the delay. I just checked and I don't have access to duke/mri

~on it :-)~

Fixed!

kiristern commented 1 year ago

@jcohenadad data is uploaded to duke/temp/kiri/bidsify. i wasn't sure what to assign to Author in the json key, so left it blank for now.

kiristern commented 1 year ago

wondering about issue 1202? I guess for now since no changes have been established, keeping as is. (However, I just realized the file names contain caps — I’ll modify that tmrw and re-upload with the corrected file names)

jcohenadad commented 1 year ago

@kiristern Thank you for curating the data. I looked at them and the file name does not correspond to the BIDS convention. For example, here's what you created:

sub-P036_MP2R_INsIDER_SCT_Seg_COR.nii.gz

whereas it should look like this one (from our already existing database):

sub-P001_UNIT1.nii.gz

Also, the JSON file has the extention nii.json instead of json.

Also, I suggest you use an already existing script to BIDSify the data (the same that was used for generating the initial 35 patients data, located under scripts/ in the BIDS dataset). Notably, there is a script called curate_basel_additional_data.py, so you could give it a try, and modify it if needed? And then, pls put it under a script/ folder in the dataset you share under duke so we make sure to include your modified script

kiristern commented 1 year ago

ahh sorry, i misunderstood. i filtered out the duplicate patients based on the same sub-PXXX but didn't realize that the file ending needed to match as well.. makes sense. thanks for noticing the .nii.json too. I'll update this evening.

oh i used the curate_basel.py not _additional_.

jcohenadad commented 1 year ago

No worries, let me know when I can review it again 😊

kiristern commented 1 year ago

Okay, fixed. but before uploading to server for review, just want to confirm whether "Author" should be the same as the person indicated in the curate_basel_additional_data.py script, or leave blank?

jcohenadad commented 1 year ago

Okay, fixed. but before uploading to server for review, just want to confirm whether "Author" should be the same as the person indicated in the curate_basel_additional_data.py script, or leave blank?

good question. I've just emailed our collaborators to ask. Once we have the answer, please make sure to not edit the py. file, but instead create a new one that will be specific to this dataset. Eg: curate_basel_additional_data_20221028.py and edit the comment at the top of the python file with the relevant info-- thanks

kiristern commented 1 year ago

sounds good, thanks. And yes, I actually made a new script and saved in on a new branch in the model_seg_ms_mp2rage repo

jcohenadad commented 1 year ago

sounds good, thanks. And yes, I actually made a new script and saved in on a new branch in the model_seg_ms_mp2rage repo

could you please open a PR? I already have some comments to give on the script

jcohenadad commented 1 year ago

Follow-up on https://github.com/ivadomed/model_seg_ms_mp2rage/issues/49#issuecomment-1294986243, both the SC segmentations and MS lesion segmentations were performed by "Tsagkas Charidimos".

kiristern commented 1 year ago

okay i uploaded the corrected data with Tsagkas Charidimos as the author to duke/temp/kiri/bidsify and i'll create a PR now

jcohenadad commented 1 year ago

Done 😊

ivadomed / model_seg_ms_mp2rage

Train model with new datasets #49