Closed alexfoias closed 2 years ago
For the moment I have pushed T1w images for the data that we received with face. @renelabounek Do you mind taking a look to QC the defacing ? thanks.
Sure, @mbondy023 and I can look at the images within this week. How can I get the pictures on our server? Three tweaks that I do not know how to solve to get the images:
1/ On the server, we have downloaded this fork of the database: https://github.com/renelabounek/data-multi-subject (which is up-to-date with the master database) How can I switch to af/fix_defaced_images branch from this fork?
2/ When I do, do I need to call some git-annex update to get the updated images on the server?
3/ Do you have a list of updated files? Or should we check all files listed in #115?
@renelabounek You would have to clone this repo.
After that you have to do:
git checkout af/fix_defaced_images
git annex get .
Then look at the branch to see if it looks right to you.
To investigate what changed:
git log --stat master..HEAD # to see filenames
git log -p master..HEAD # to see content, commit-by-commit
git diff master..HEAD # to see content, overall
The updated files are:
@alexfoias Ok, thanks for the manual. I will clone the database tomorrow. On Thursday, I have meeting with Monica when we make visual inspection of updated scans and let you know.
@alexfoias: @mbondy023 and I have checked several scans. All appeared defaced fine with no loss in brain tissue volume. @mbondy023 will re-calculate freesurfer analysis on these scans and simultaneously check the defacing quality of each updated scan. Please, would it be possible to enable her to edit this particular comment: https://github.com/spine-generic/data-multi-subject/issues/115#issuecomment-1030220637? I was not able to give her the permission.
@kousu is it possible to give access to a edit right for this particular comment: #115 (comment) to a user ?
@kousu is it possible to give access to a edit right for this particular comment: #115 (comment) to a user ?
I don't think there's a way without granting membership, and we're pretty careful about permissions around this particular dataset.
Instead, I've got a basic workaround at https://github.com/spine-generic/data-multi-subject/issues/115#issuecomment-1065297685
@kousu thanks for the input.
@renelabounek I have pushed the new images on https://github.com/spine-generic/data-multi-subject/pull/119/commits/5e1d353a96c4824dc92e080f2cc18d25631e1594. Could you please review them ? thanks.
@renelabounek I have pushed the new images on https://github.com/spine-generic/data-multi-subject/commit/5e1d353a96c4824dc92e080f2cc18d25631e1594. Could you please review them ? thanks.
I have reviewed all cmrr scans and geneva04. All appears fine. Previous updates @mbondy023 approved. Regrading the comment https://github.com/spine-generic/data-multi-subject/issues/115#issuecomment-1065334918, many T1w scans with defacing issue remain. Should I start to email contributors? It does not appear like just a 2-week issue to fully finish it.
@renelabounek I have pushed the new images on 5e1d353. Could you please review them ? thanks.
I have reviewed all cmrr scans and geneva04. All appears fine. Previous updates @mbondy023 approved. Regrading the comment #115 (comment), many T1w scans with defacing issue remain. Should I start to email contributors? It does not appear like just a 2-week issue to fully finish it.
I would not contact contributors, because many of them moved on to other projects/institutions and we might end up spending lots of time/efforts to hunt after them, and explain what is needed, what is defacing, explaining how to do it, and then review it ourselves, etc.
i think, timewise, it will be more effective if @alexfoias finishes up the defacing job (and @renelabounek if your team can help with that it would be awesome, maybe we could split the work)
for the remaining sites, we received the images already defaced. I have only pushed the images that we had on our server and which were received with the face.
for the remaining sites, we received the images already defaced. I have only pushed the images that we had on our server and which were received with the face.
ok, so indeed, we need to contact the contributors, @renelabounek would you mind doing it? thanks!! 🙏
@jcohenadad I agree to close this PR but not the Issue #115. There is about 14 sites where are issues with the T1w defacing. I will email contributors of the particular sites with the request and cc you.
@jcohenadad I agree to close this PR
I assume you meant 'merge and close' the PR (ie: we want to keep the changes made by @alexfoias). If that's the case, then yes, let's merge and close, and we will follow-up #115 in a subsequent PR.
@jcohenadad I agree to close this PR
I assume you meant 'merge and close' the PR (ie: we want to keep the changes made by @alexfoias). If that's the case, then yes, let's merge and close, and we will follow-up #115 in a subsequent PR.
Oh sorry, if you waited for ym response :-X Yes, that is what I meant.
Fixes https://github.com/spine-generic/data-multi-subject/issues/115