Fix wrong defacing in some images

[alexfoias]

This PR fixes the remaining issues with defacing. Fixes #22

[alexfoias]

@jcohenadad This PR is ready for review.

[alexfoias]

Fixed in https://github.com/spine-generic/data-multi-subject/pull/19/commits/0b2399908b823deb0125df70fde74f9547e8da89

[alexfoias]

The issues signalled here: https://github.com/spine-generic/data-multi-subject/pull/21#issuecomment-667390603

• sub-cmrra02: fixed T2w
• sub-cmrra04 & sub-cmrra05 : we received the T2w images like that.
• sub-oxfordFmrib07: fixed T1w
• sub-dresden02: fixed T2w
• sub-stanford06: fixed T1w

[jcohenadad]

@alexfoias the image shown in https://github.com/spine-generic/data-multi-subject/pull/19#issue-460200227 is not representative of the problem (it is representative of the solution)--

[jcohenadad]

• sub-cmrra04 & sub-cmrra05 : we received the T2w images like that.

@alexfoias are you sure? sub-cmrra02_T2w.nii.gz , which you were able to fix, is coming from the same site

[alexfoias]

The data that we have from the backup look like this:

[jcohenadad]

and how does sub-cmrra02_T2w.nii.gz look like? are the other files in the backup not defaced?

[alexfoias]

All the data from cmrr* came defaced.

[jcohenadad]

All the data from cmrr* came defaced.

so how come you were able to "reface" cmrra02?

also see my other question https://github.com/spine-generic/data-multi-subject/pull/19#issuecomment-668058959 are the other files in the backup not defaced?

[alexfoias]

cmrra02 wasn't refaced. The initial file wasn't as chopped as the one that we uploaded before. All the data from cmrr are defaced. Here is a QC of the data from the recovered backup (before defacing of the complete multiSubject).

[jcohenadad]

cmrra02 wasn't refaced

All the data from cmrr* came defaced.

🧐

[alexfoias]

I mixed up things on my fork. I'll close this PR and open a new one with the clean changes.