Adding manual centerlines #204

jcohenadad · 2023-01-18T21:44:44Z

hi!

EDIT: The branch with the latest (corrected) centerlines is ks/troubleshoot. New branch was created due to a mix up. Future updates will only be this branch!

The text was updated successfully, but these errors were encountered:

jcohenadad · 2023-01-18T21:51:42Z

problem identified in sub-04/ses-01: centerline is incomplete:

kiristern · 2023-01-19T03:06:56Z

went through the subjects and fixed the centerlines. if @naga-karthik you want to quickly check a few random sub to confirm it's okay? thanks!

naga-karthik · 2023-01-19T21:04:53Z

I checked a few more subjects and lgtm! So, the latest branch (with the fixed centrelines) is ks/centerlines.

naga-karthik · 2023-01-19T21:14:50Z

@jcohenadad could you please merge the latest updates from the branch that's mentioned in this comment?

jcohenadad · 2023-01-19T21:16:05Z

@naga-karthik @kiristern thanks for looking into this! can you please work on a single branch and update the issue so there is no confusion as to what branch to use (two branches are listed in this issue)-- thanks!

jcohenadad · 2023-01-19T21:24:34Z

currently reviewing ks/centerlines. Any reasons you included the CSV files?

.../anat/sub-zh04_ses-01_acq-sag_T2w_centerline-manual.csv      |  717 +++++++------
 .../anat/sub-zh04_ses-01_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh05_ses-01_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../sub-zh05/sub-zh05_ses-01_acq-sag_T2w_centerline-manual.csv  |  308 ++++++
 .../anat/sub-zh06_ses-01_acq-sag_T2w_centerline-manual.csv      |  975 ++++++++---------
 .../anat/sub-zh06_ses-01_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh06_ses-02_acq-sag_T2w_centerline-manual.csv      | 1022 +++++++++---------
 .../anat/sub-zh06_ses-02_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh09_ses-01_acq-sag_T2w_centerline-manual.csv      |  818 +++++++-------
 .../anat/sub-zh09_ses-01_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh11_ses-01_acq-sag_T2w_centerline-manual.csv      | 1004 +++++++++---------
 .../anat/sub-zh11_ses-01_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh11_ses-02_acq-sag_T2w_centerline-manual.csv      | 1004 +++++++++---------
 .../anat/sub-zh11_ses-02_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh14_ses-01_acq-sag_T2w_centerline-manual.csv      |  858 +++++++--------
 .../anat/sub-zh14_ses-01_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh16_ses-01_acq-sag_T2w_centerline-manual.csv      | 1021 +++++++++---------
 .../anat/sub-zh16_ses-01_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh22_ses-01_acq-sag_T2w_centerline-manual.csv      |  858 +++++++--------
 .../anat/sub-zh22_ses-01_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh36_ses-01_acq-sag_T2w_centerline-manual.csv      |  784 +++++++-------
 .../anat/sub-zh36_ses-01_acq-sag_T2w_centerline-manual.nii.gz   |    2 +-
 .../anat/sub-zh37_ses-01_acq-sag_T2w_centerline-manual.csv      |  962 ++++++++---------

jcohenadad · 2023-01-19T21:30:02Z

My review:

sub-zh04/ses-01 ✅
sub-zh05/ses-01 ✅
sub-zh06/ses-01 ❌

details

You can go a bit higher (C1 is only partially covered by the centerline)
sub-zh09/ses-01 ✅

jcohenadad · 2023-01-19T21:31:09Z

mistake on file location: sci-zurich/derivatives/labels/sub-zh05/sub-zh05_ses-01_acq-sag_T2w_centerline-manual.csv

kiristern · 2023-01-19T23:37:40Z

i rm all csv files, as they should not have been incl. and fixed sub-zh06/ses-01

jcohenadad · 2023-01-20T03:18:34Z

@kiristern I reviewed 9eab8de77d132a886c3e0b091a4e100e990751f8:

wrong file location: sub-zh16/ses-01/anat/sub-zh16_ses-01_acq-sag_T2w_centerline.nii.gz
sub-zh22/ses-01 ✅
sub-zh49_ses-01 ✅

jcohenadad · 2023-01-20T03:26:50Z

@kiristern @naga-karthik can you please delete the branch nk/add_manual_centerline (no need to waste physical space and accumulate unnecessary history) and remove its mention here: #204 (comment) (instead of the EDIT)

kiristern · 2023-01-20T14:47:05Z

wrong file location: sub-zh16/ses-01/anat/sub-zh16_ses-01_acq-sag_T2w_centerline.nii.gz

My mistake, thanks for catching! i moved it to the appropriate derivative folder and also reverted the .csv files because @naga-karthik suggested they could be used for training a regression model

kiristern · 2023-01-20T17:17:20Z

@jcohenadad we were having some issues pulling the changes so I created a new branch ks/troubleshoot which has all the good files and changes, if you could use that instead to merge to master.

I'm not going to delete the ks/centerlines branch just yet, since we want to understand why @naga-karthik isn't able to retrieve the files on ks/centerlines nor ks/troubleshoot (when he git pull && git annex sync --no-content && git annex get . it deleted them -- see the log on ks/centerlines). Jan was able to retrieve the files on ks/troubleshoot

jcohenadad · 2023-01-20T17:55:03Z

hum... maybe @mguaypaq or @kousu can help with these git-annex issues. But on my end I could see the changes, and they can be merged on master whenever you like (so others should also be able to see them once they pull master).

naga-karthik · 2023-01-20T18:45:31Z

Sure, if it works on your end, please merge it to master @jcohenadad ! I'll do the surgery on the branch by discussing with @mguaypaq next week. Seems like the problem is specific to me.

naga-karthik · 2023-01-20T18:47:59Z

Just to make sure, the latest branch is ks/troubleshoot (also updated in the first comment on the issue)

mguaypaq · 2023-01-23T17:32:04Z

Just an update: I think we've isolated the problem, which is that git annex behaves weirdly on duke. Now @naga-karthik has a clean working copy of the repository outside duke, so hopefully things will work better.

naga-karthik · 2023-01-23T17:49:24Z

@jcohenadad if not already done, can you please merge the branch ks/troubleshoot to master so that the additional branches can be deleted? Thank you!

jcohenadad · 2023-01-23T18:12:09Z

not done-- will do-- on my todo list-- other priorities

jcohenadad · 2023-01-24T02:50:24Z

ks/troubleshoot is not up-to-date with master:

fccc609aeb3336e8d6978306cb0b24db7d825eb3 (HEAD -> master, origin/master, origin/HEAD) modified segmentation

jcohenadad · 2023-01-24T02:52:34Z

Bringing it up-to-date:

Terminal output

julien-macbook:~/data.neuro/sci-zurich $ git merge master          
Merge made by the 'recursive' strategy.
 derivatives/labels/sub-zh56/ses-01/anat/sub-zh56_ses-01_acq-sag_T2w_lesion-manual.json   | 2 +-
 derivatives/labels/sub-zh56/ses-01/anat/sub-zh56_ses-01_acq-sag_T2w_lesion-manual.nii.gz | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)
julien-macbook:~/data.neuro/sci-zurich $ git pull && git annex sync --no-content
hint: Pulling without specifying how to reconcile divergent branches is
hint: discouraged. You can squelch this message by running one of the following
hint: commands sometime before your next pull:
hint: 
hint:   git config pull.rebase false  # merge (the default strategy)
hint:   git config pull.rebase true   # rebase
hint:   git config pull.ff only       # fast-forward only
hint: 
hint: You can replace "git config" with "git config --global" to set a default
hint: preference for all repositories. You can also pass --rebase, --no-rebase,
hint: or --ff-only on the command line to override the configured default per
hint: invocation.
Already up to date.
commit 
On branch ks/troubleshoot
Your branch is ahead of 'origin/ks/troubleshoot' by 2 commits.
  (use "git push" to publish your local commits)

nothing to commit, working tree clean
ok
pull origin 
ok
push origin 
Enumerating objects: 10, done.
Counting objects: 100% (10/10), done.
Delta compression using up to 12 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (4/4), 405 bytes | 405.00 KiB/s, done.
Total 4 (delta 2), reused 0 (delta 0), pack-reused 0
To data.neuro.polymtl.ca:datasets/sci-zurich
 * [new branch]      ks/troubleshoot -> synced/ks/troubleshoot
ok

Looking good:

Terminal output

julien-macbook:~/data.neuro/sci-zurich $ git diff --name-only master..HEAD
derivatives/labels/sub-zh04/ses-01/anat/sub-zh04_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh04/ses-01/anat/sub-zh04_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh05/ses-01/anat/sub-zh05_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh05/ses-01/anat/sub-zh05_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh06/ses-01/anat/sub-zh06_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh06/ses-01/anat/sub-zh06_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh06/ses-02/anat/sub-zh06_ses-02_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh06/ses-02/anat/sub-zh06_ses-02_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh09/ses-01/anat/sub-zh09_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh09/ses-01/anat/sub-zh09_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh11/ses-01/anat/sub-zh11_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh11/ses-01/anat/sub-zh11_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh11/ses-02/anat/sub-zh11_ses-02_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh11/ses-02/anat/sub-zh11_ses-02_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh14/ses-01/anat/sub-zh14_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh14/ses-01/anat/sub-zh14_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh16/ses-01/anat/sub-zh16_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh16/ses-01/anat/sub-zh16_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh22/ses-01/anat/sub-zh22_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh22/ses-01/anat/sub-zh22_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh36/ses-01/anat/sub-zh36_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh36/ses-01/anat/sub-zh36_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh37/ses-01/anat/sub-zh37_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh37/ses-01/anat/sub-zh37_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh48/ses-01/anat/sub-zh48_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh48/ses-01/anat/sub-zh48_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh49/ses-01/anat/sub-zh49_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh49/ses-01/anat/sub-zh49_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh68/ses-01/anat/sub-zh68_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh68/ses-01/anat/sub-zh68_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh69/ses-01/anat/sub-zh69_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh69/ses-01/anat/sub-zh69_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh77/ses-01/anat/sub-zh77_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh77/ses-01/anat/sub-zh77_ses-01_acq-sag_T2w_centerline-manual.nii.gz
derivatives/labels/sub-zh78/ses-01/anat/sub-zh78_ses-01_acq-sag_T2w_centerline-manual.csv
derivatives/labels/sub-zh78/ses-01/anat/sub-zh78_ses-01_acq-sag_T2w_centerline-manual.nii.gz

jcohenadad · 2023-01-24T02:57:23Z

Convenient script for QCing (replace 04 05 by start end):

for i in $(seq -f "%02g" 04 05); do fsleyes -S sub-zh${i}/ses-01/anat/sub-zh${i}_ses-01_acq-sag_T2w  derivatives/labels/sub-zh${i}/ses-01/anat/sub-zh${i}_ses-01_acq-sag_T2w_centerline-manual -cm red; done

jcohenadad · 2023-01-24T03:01:39Z

merged and cleaned up:

Terminal output

julien-macbook:~/data.neuro/sci-zurich $ git merge ks/troubleshoot
Updating fccc609..9486a83
Fast-forward
 derivatives/labels/sub-zh04/ses-01/anat/sub-zh04_ses-01_acq-sag_T2w_centerline-manual.csv    | 422 ++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh04/ses-01/anat/sub-zh04_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh05/ses-01/anat/sub-zh05_ses-01_acq-sag_T2w_centerline-manual.csv    | 308 ++++++++++++++++++++++++++++
 derivatives/labels/sub-zh05/ses-01/anat/sub-zh05_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh06/ses-01/anat/sub-zh06_ses-01_acq-sag_T2w_centerline-manual.csv    | 464 +++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh06/ses-01/anat/sub-zh06_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh06/ses-02/anat/sub-zh06_ses-02_acq-sag_T2w_centerline-manual.csv    | 511 +++++++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh06/ses-02/anat/sub-zh06_ses-02_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh09/ses-01/anat/sub-zh09_ses-01_acq-sag_T2w_centerline-manual.csv    | 409 +++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh09/ses-01/anat/sub-zh09_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh11/ses-01/anat/sub-zh11_ses-01_acq-sag_T2w_centerline-manual.csv    | 511 +++++++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh11/ses-01/anat/sub-zh11_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh11/ses-02/anat/sub-zh11_ses-02_acq-sag_T2w_centerline-manual.csv    | 511 +++++++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh11/ses-02/anat/sub-zh11_ses-02_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh14/ses-01/anat/sub-zh14_ses-01_acq-sag_T2w_centerline-manual.csv    | 447 ++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh14/ses-01/anat/sub-zh14_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh16/ses-01/anat/sub-zh16_ses-01_acq-sag_T2w_centerline-manual.csv    | 510 +++++++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh16/ses-01/anat/sub-zh16_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh22/ses-01/anat/sub-zh22_ses-01_acq-sag_T2w_centerline-manual.csv    | 447 ++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh22/ses-01/anat/sub-zh22_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh36/ses-01/anat/sub-zh36_ses-01_acq-sag_T2w_centerline-manual.csv    | 375 ++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh36/ses-01/anat/sub-zh36_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh37/ses-01/anat/sub-zh37_ses-01_acq-sag_T2w_centerline-manual.csv    | 481 +++++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh37/ses-01/anat/sub-zh37_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh48/ses-01/anat/sub-zh48_ses-01_acq-sag_T2w_centerline-manual.csv    | 761 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh48/ses-01/anat/sub-zh48_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh49/ses-01/anat/sub-zh49_ses-01_acq-sag_T2w_centerline-manual.csv    | 372 +++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh49/ses-01/anat/sub-zh49_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh68/ses-01/anat/sub-zh68_ses-01_acq-sag_T2w_centerline-manual.csv    | 366 +++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh68/ses-01/anat/sub-zh68_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh69/ses-01/anat/sub-zh69_ses-01_acq-sag_T2w_centerline-manual.csv    | 447 ++++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh69/ses-01/anat/sub-zh69_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh77/ses-01/anat/sub-zh77_ses-01_acq-sag_T2w_centerline-manual.csv    | 340 ++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh77/ses-01/anat/sub-zh77_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 derivatives/labels/sub-zh78/ses-01/anat/sub-zh78_ses-01_acq-sag_T2w_centerline-manual.csv    | 442 +++++++++++++++++++++++++++++++++++++++
 derivatives/labels/sub-zh78/ses-01/anat/sub-zh78_ses-01_acq-sag_T2w_centerline-manual.nii.gz |   1 +
 36 files changed, 8142 insertions(+)
 create mode 100644 derivatives/labels/sub-zh04/ses-01/anat/sub-zh04_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh04/ses-01/anat/sub-zh04_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh05/ses-01/anat/sub-zh05_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh05/ses-01/anat/sub-zh05_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh06/ses-01/anat/sub-zh06_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh06/ses-01/anat/sub-zh06_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh06/ses-02/anat/sub-zh06_ses-02_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh06/ses-02/anat/sub-zh06_ses-02_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh09/ses-01/anat/sub-zh09_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh09/ses-01/anat/sub-zh09_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh11/ses-01/anat/sub-zh11_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh11/ses-01/anat/sub-zh11_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh11/ses-02/anat/sub-zh11_ses-02_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh11/ses-02/anat/sub-zh11_ses-02_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh14/ses-01/anat/sub-zh14_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh14/ses-01/anat/sub-zh14_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh16/ses-01/anat/sub-zh16_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh16/ses-01/anat/sub-zh16_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh22/ses-01/anat/sub-zh22_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh22/ses-01/anat/sub-zh22_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh36/ses-01/anat/sub-zh36_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh36/ses-01/anat/sub-zh36_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh37/ses-01/anat/sub-zh37_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh37/ses-01/anat/sub-zh37_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh48/ses-01/anat/sub-zh48_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh48/ses-01/anat/sub-zh48_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh49/ses-01/anat/sub-zh49_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh49/ses-01/anat/sub-zh49_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh68/ses-01/anat/sub-zh68_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh68/ses-01/anat/sub-zh68_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh69/ses-01/anat/sub-zh69_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh69/ses-01/anat/sub-zh69_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh77/ses-01/anat/sub-zh77_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh77/ses-01/anat/sub-zh77_ses-01_acq-sag_T2w_centerline-manual.nii.gz
 create mode 100644 derivatives/labels/sub-zh78/ses-01/anat/sub-zh78_ses-01_acq-sag_T2w_centerline-manual.csv
 create mode 100644 derivatives/labels/sub-zh78/ses-01/anat/sub-zh78_ses-01_acq-sag_T2w_centerline-manual.nii.gz
julien-macbook:~/data.neuro/sci-zurich $ git push
Total 0 (delta 0), reused 0 (delta 0), pack-reused 0
To data.neuro.polymtl.ca:datasets/sci-zurich
   fccc609..9486a83  master -> master
julien-macbook:~/data.neuro/sci-zurich $ git branch -d ks/troubleshoot
Deleted branch ks/troubleshoot (was 9486a83).
julien-macbook:~/data.neuro/sci-zurich $ git push origin :ks/troubleshoot                  
To data.neuro.polymtl.ca:datasets/sci-zurich
 - [deleted]         ks/troubleshoot

jcohenadad · 2023-01-24T03:03:00Z

Additional cleanup

Terminal output

julien-macbook:~/data.neuro/sci-zurich $ gb
  git-annex
  ks/centerlines
* master
  synced/ks/centerlines
  synced/ks/troubleshoot
  synced/master
julien-macbook:~/data.neuro/sci-zurich $ git branch -d ks/centerlines
warning: deleting branch 'ks/centerlines' that has been merged to
         'refs/remotes/origin/ks/centerlines', but not yet merged to HEAD.
Deleted branch ks/centerlines (was 8d79a4b).
julien-macbook:~/data.neuro/sci-zurich $ git push origin :ks/centerlines
To data.neuro.polymtl.ca:datasets/sci-zurich
 - [deleted]         ks/centerlines
julien-macbook:~/data.neuro/sci-zurich $ git branch -d synced/ks/centerlines
Deleted branch synced/ks/centerlines (was fbfdde7).
julien-macbook:~/data.neuro/sci-zurich $ git push origin :synced/ks/centerlines
To data.neuro.polymtl.ca:datasets/sci-zurich
 - [deleted]         synced/ks/centerlines
julien-macbook:~/data.neuro/sci-zurich $ git branch -d synced/ks/troubleshoot
Deleted branch synced/ks/troubleshoot (was 9486a83).
julien-macbook:~/data.neuro/sci-zurich $ git push origin :synced/ks/troubleshoot
To data.neuro.polymtl.ca:datasets/sci-zurich
 - [deleted]         synced/ks/troubleshoot
julien-macbook:~/data.neuro/sci-zurich $ gb
  git-annex
* master
  synced/master

naga-karthik · 2023-03-30T11:48:06Z

After running sct_get_centerline on the latest cohort of 16 more subjects, I found an error with sub-zh87. I had to manually create the centerline using the steps mentioned here. This can be found under my branch nk/manual_centerline_new_cohort. Here's how the manual correction looks:

@mguaypaq can you please merge it to master? Thanks in advance!

jcohenadad · 2023-03-30T13:11:20Z

it would be really nice to have a proper QC for centerline, ie: where we can see it from top to bottom without interruption. Tagging @joshuacwnewton so he is aware of this feature request (i think we already have an issue open about this)

naga-karthik · 2023-03-30T15:01:20Z

Agreed!

Thanks to @valosekj's suggestion, I use sct_label_vertebrae while running sct_qc as a workaround to visualize the centerline on the sagittal plane (check this to see how it is run). The result is quite decent and it looks something like the one shown below:

Workaround QC

joshuacwnewton · 2023-03-30T16:17:14Z

Tagging @joshuacwnewton so he is aware of this feature request (i think we already have an issue open about this)

Expand centerline QC report to add sagittal/coronal views spinalcordtoolbox/spinalcordtoolbox#4011

In that issue, @valosekj describes the exact same workaround that @naga-karthik has mentioned above.

mguaypaq · 2023-04-03T19:17:43Z

This can be found under my branch nk/manual_centerline_new_cohort. [...]
@mguaypaq can you please merge it to master? Thanks in advance!

Done! git annex get is happy, so I merged into master.

valosekj · 2023-06-23T14:11:32Z

Closing since the branch was merged into master.
Moreover, we have now also SC segmentations, see #238

jcohenadad added the dataset: sci-zurich label Jan 18, 2023

jcohenadad assigned naga-karthik Jan 18, 2023

jcohenadad closed this as completed Jan 24, 2023

naga-karthik reopened this Mar 30, 2023

valosekj closed this as completed Jun 23, 2023

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Adding manual centerlines #204

Adding manual centerlines #204

jcohenadad commented Jan 18, 2023 •

edited by naga-karthik

Loading

jcohenadad commented Jan 18, 2023

kiristern commented Jan 19, 2023

naga-karthik commented Jan 19, 2023

naga-karthik commented Jan 19, 2023

jcohenadad commented Jan 19, 2023 •

edited

Loading

jcohenadad commented Jan 19, 2023

jcohenadad commented Jan 19, 2023 •

edited

Loading

jcohenadad commented Jan 19, 2023

kiristern commented Jan 19, 2023

jcohenadad commented Jan 20, 2023 •

edited

Loading

jcohenadad commented Jan 20, 2023

kiristern commented Jan 20, 2023

kiristern commented Jan 20, 2023

jcohenadad commented Jan 20, 2023

naga-karthik commented Jan 20, 2023

naga-karthik commented Jan 20, 2023

mguaypaq commented Jan 23, 2023

naga-karthik commented Jan 23, 2023 •

edited

Loading

jcohenadad commented Jan 23, 2023

jcohenadad commented Jan 24, 2023

jcohenadad commented Jan 24, 2023 •

edited

Loading

jcohenadad commented Jan 24, 2023

jcohenadad commented Jan 24, 2023

jcohenadad commented Jan 24, 2023

naga-karthik commented Mar 30, 2023

jcohenadad commented Mar 30, 2023 •

edited

Loading

naga-karthik commented Mar 30, 2023

joshuacwnewton commented Mar 30, 2023 •

edited

Loading

mguaypaq commented Apr 3, 2023

valosekj commented Jun 23, 2023

Adding manual centerlines #204

Adding manual centerlines #204

Comments

jcohenadad commented Jan 18, 2023 • edited by naga-karthik Loading

jcohenadad commented Jan 18, 2023

kiristern commented Jan 19, 2023

naga-karthik commented Jan 19, 2023

naga-karthik commented Jan 19, 2023

jcohenadad commented Jan 19, 2023 • edited Loading

jcohenadad commented Jan 19, 2023

jcohenadad commented Jan 19, 2023 • edited Loading

jcohenadad commented Jan 19, 2023

kiristern commented Jan 19, 2023

jcohenadad commented Jan 20, 2023 • edited Loading

jcohenadad commented Jan 20, 2023

kiristern commented Jan 20, 2023

kiristern commented Jan 20, 2023

jcohenadad commented Jan 20, 2023

naga-karthik commented Jan 20, 2023

naga-karthik commented Jan 20, 2023

mguaypaq commented Jan 23, 2023

naga-karthik commented Jan 23, 2023 • edited Loading

jcohenadad commented Jan 23, 2023

jcohenadad commented Jan 24, 2023

jcohenadad commented Jan 24, 2023 • edited Loading

jcohenadad commented Jan 24, 2023

jcohenadad commented Jan 24, 2023

jcohenadad commented Jan 24, 2023

naga-karthik commented Mar 30, 2023

jcohenadad commented Mar 30, 2023 • edited Loading

naga-karthik commented Mar 30, 2023

joshuacwnewton commented Mar 30, 2023 • edited Loading

mguaypaq commented Apr 3, 2023

valosekj commented Jun 23, 2023

jcohenadad commented Jan 18, 2023 •

edited by naga-karthik

Loading

jcohenadad commented Jan 19, 2023 •

edited

Loading

jcohenadad commented Jan 19, 2023 •

edited

Loading

jcohenadad commented Jan 20, 2023 •

edited

Loading

naga-karthik commented Jan 23, 2023 •

edited

Loading

jcohenadad commented Jan 24, 2023 •

edited

Loading

jcohenadad commented Mar 30, 2023 •

edited

Loading

joshuacwnewton commented Mar 30, 2023 •

edited

Loading