Fixing issue #68 by generating a centerline NIFTI file for subjects who do not have a SC mask NIFTI file

[NadiaBlostein]

Fixing issue #68: In preprocess_normalize.py, the straighten_all_subjects() method requires for each subject to either have a SC mask NIFTI file (*_label-SC_mask.nii.gz) or a centerline NIFTI file (*_label-centerline.nii.gz). The current PR allows for preprocess_normalize.py to generate a centerline NIFTI file for each subject that has neither a SC mask NIFTI file nor a centerline NIFTI file.

Fixes #70

[NadiaBlostein]

title + body of the PR should be "human readable" as i said multiple times in the past-- @rohanbanerjee will review/modify first, then I review

Is this better?

[NadiaBlostein]

@jcohenadad will do tomorrow am

@rohanbanerjee If you read this part of the code, the straightening should not work if there is no SC mask NIFTI file or centerline NIFTI file to read in. Am I missing something?

Cheers

[jcohenadad]

@jcohenadad will do tomorrow am

in the interest of time, @rohanbanerjee can you please do it now so we can merge

[rohanbanerjee]

@NadiaBlostein Yes indeed, the straighten_all_subjects() method would not work if there is not SC mask or centerline file. But the point that I made was that no user should run the preprocess_normalize.py until they have confirmed that there is a SC/centerline present for each and every subject they have -- which is step 1.3. They should run step 1.6 which is running the preprocess_normalize.py after 1.3 and also possibly after qc (step 1.4)

[jcohenadad]

@rohanbanerjee as per https://github.com/neuropoly/template/pull/69/commits/16fa7569dd37a0fa54b4f3a35be3d7e7cc187205, make sure to ALWAYS update the PR body according to our conventions. I did it for you:

but please in the future follow our directives

[jcohenadad]

Testing this PR with the dog data. Data: duke/temp/rohan/bids_data Code: 16fa7569dd37a0fa54b4f3a35be3d7e7cc187205 config file:

{
    "path_data": "PATH_TO_BIDS_DATA",
    "include-list": "sub-HarshmanDobby",
    "data_type": "anat",
    "contrast": "t2",
    "suffix_image": "_T2",
    "first_disc": "1",
    "last_disc": "26"
}

[rohanbanerjee]

Hello @NadiaBlostein, did you decide about this PR? Could you please go ahead with either closing it or merging it. I am waiting on this PR for a few other PRs that I would like to open.

[NadiaBlostein]

Hey! I'm working on my other lab project this week and moving out of the country. Aren't other people now working on this?

[NadiaBlostein]

@rohanbanerjee I'll just merge this one because all the issues with it that were mentioned in the last meeting have been opened as separate issues