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neuropoly / data-management

Repo that deals with datalad aspects for internal use
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add data `sub-56027` to `sct-testing-large` #164

Open alexfoias opened 2 years ago

alexfoias commented 2 years ago

I pushed the data from email Using sct for Quantitative Analysis of Spinal Cord MRI received on December 18, 2021 9:14:47 PM on the branch af/add_sub-56027 under datasets/sct-testing-large.

Here is a git log:

commit 38fd2fc3df032546a5cd361fd3a7cf5589e5cf5c (HEAD -> af/add_sub-56027)
Author: Alexandru Foias <afoias@polymtl.ca>
Date:   Thu Jan 6 15:41:29 2022 -0500

    add sub-56027

 .../sub-56027_ses-20180207_acq-sagcerv_T2w_labeled-lesion-manual.nii.gz |    1 +
 .../sub-56027_ses-20180207_acq-sagcerv_T2w_labeled-seg-manual.nii.gz    |    1 +
 .../sub-56027_ses-20180207_acq-sagcerv_T2w_labels-disc-manual.nii.gz    |    1 +
 ...-56027_ses-20180207_acq-sagcervstir_T2w_labeled-lesion-manual.nii.gz |    1 +
 .../sub-56027_ses-20180207_acq-sagcervstir_T2w_lesion-manual.nii.gz     |    1 +
 .../anat/sub-56027_ses-20180207_acq-sagcervstir_T2w_seg-manual.nii.gz   |    1 +
 participants.tsv                                                        | 3147 ++++++++++++++++----------------
 sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w.json |   62 +
 .../ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w.nii.gz     |    1 +
 .../ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w.json   |   63 +
 .../ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w.nii.gz |    1 +
 11 files changed, 1707 insertions(+), 1573 deletions(-)
(END)
alexfoias commented 2 years ago

@jcohenadad Here is the issue the you requested.

jcohenadad commented 2 years ago

I see the added character "^M":

+participant_id sex     age     first_name      last_name       date_of_birth   date_of_scan    pathology       data_id institution_id^M
+sub-56027      n/a     n/a     n/a     n/a     n/a     n/a     n/a     n/a     n/a^M
+sub-amuAMU15001        n/a     n/a     unknown unknown n/a     n/a     HC      amu_T2star-AMU15_G1-1   amuAMU15^M
+sub-amuAMU15002        n/a     n/a     unknown unknown n/a     n/a     HC      amu_T2star-AMU15_G1-10  amuAMU15^M
+sub-amuAMU15003        n/a     n/a     unknown unknown n/a     n/a     HC      amu_T2star-AMU15_G1-11  amuAMU15^M
jcohenadad commented 2 years ago

what is the difference between:

sub-56027_ses-20180207_acq-sagcervstir_T2w_labeled-lesion-manual.nii.gz

and 

sub-56027_ses-20180207_acq-sagcervstir_T2w_lesion-manual.nii.gz
jcohenadad commented 2 years ago

"institution_id" should be indicated: "ShebaMedicalCenterIsrael"

jcohenadad commented 2 years ago

"pathology" --> MS

jcohenadad commented 2 years ago

for easier identification i would rename sub ID as: sub-israelSheba56027

jcohenadad commented 2 years ago

in the JSON metadata fields i would add a link to this issue for keeping provenance

alexfoias commented 2 years ago

@jcohenadad I have fixed the issues raised above.

Concerning the **labeled-*** files from https://github.com/neuropoly/data-management/issues/164#issuecomment-1006967875 : I think labeled means that each lesion has a different level of grey, not sure if this info is useful for us. Screen Shot 2022-01-07 at 10 29 49 AM Screen Shot 2022-01-07 at 10 29 32 AM

jcohenadad commented 2 years ago

@jcohenadad I have fixed the issues raised above.

thanks!

Concerning the labeled-* files from #164 (comment) : I think labeled means that each lesion has a different level of grey, not sure if this info is useful for us.

indeed, this is not useful. We should only keep the binary labels

alexfoias commented 2 years ago

@jcohenadad I removed the l**abeled-*** files. Please let me know if I can merge. thanks

commit 4240d554ccfc3c3433cff7e2af3514209457003b (HEAD -> af/add_sub-56027, origin/af/add_sub-56027)
Author: Alexandru Foias <afoias@polymtl.ca>
Date:   Fri Jan 7 16:04:29 2022 -0500

    remove labeled data

 .../anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labeled-lesion-manual.nii.gz      | 1 -
 .../anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labeled-seg-manual.nii.gz         | 1 -
 .../anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w_labeled-lesion-manual.nii.gz  | 1 -
 3 files changed, 3 deletions(-)
alexfoias commented 2 years ago

@jcohenadad Could you please review the branch ? Thank you.

jcohenadad commented 2 years ago

@alexfoias i'm looking into your branch now.

since it's been a while, i am just wondering if your branch is up to date with master?

alexfoias commented 2 years ago

@kousu I'm not sure if we have a procedure to update the branch with master. I have tried the following commands. Please let me know if I have to do something different.

I did this to make sure I'm up to date with master:

git checkout master
git pull
git annex sync --no-content
git annex get .
git checkout af/add_sub-56027
git merge origin/master
git merge origin/master
git push origin af/add_sub-56027
git log --stat master..HEAD

Here is the output:

commit 4240d554ccfc3c3433cff7e2af3514209457003b (HEAD -> af/add_sub-56027, origin/af/add_sub-56027)
Author: Alexandru Foias <afoias@polymtl.ca>
Date:   Fri Jan 7 16:04:29 2022 -0500

    remove labeled data

 derivatives/labels/sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labeled-lesion-manual.nii.gz     | 1 -
 derivatives/labels/sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labeled-seg-manual.nii.gz        | 1 -
 derivatives/labels/sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w_labeled-lesion-manual.nii.gz | 1 -
 3 files changed, 3 deletions(-)

commit 969354cfb321786bda342843fe624fd9e540b59a
Author: Alexandru Foias <afoias@polymtl.ca>
Date:   Fri Jan 7 11:25:47 2022 -0500

    fix ^M

 participants.tsv | 3146 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++---------------------------------------------------------------------
 1 file changed, 1573 insertions(+), 1573 deletions(-)

commit f2d4de0d43d5d4c99e4ed9833994553b044e1e92
Author: Alexandru Foias <afoias@polymtl.ca>
Date:   Fri Jan 7 10:36:03 2022 -0500

    rename subject

 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labeled-lesion-manual.nii.gz}                                                       | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labeled-seg-manual.nii.gz}                                                          | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labels-disc-manual.nii.gz}                                                          | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w_labeled-lesion-manual.nii.gz}                                                   | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w_lesion-manual.nii.gz}                                                           | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w_seg-manual.nii.gz}                                                              | 0
 participants.tsv                                                                                                                                            | 2 +-
 .../anat/sub-56027_ses-20180207_acq-sagcerv_T2w.json => sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w.json       | 2 +-
 .../anat/sub-56027_ses-20180207_acq-sagcerv_T2w.nii.gz => sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w.nii.gz   | 0
 .../sub-56027_ses-20180207_acq-sagcervstir_T2w.json => sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w.json    | 2 +-
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w.nii.gz                                                                          | 0
 11 files changed, 3 insertions(+), 3 deletions(-)

commit 38fd2fc3df032546a5cd361fd3a7cf5589e5cf5c
Author: Alexandru Foias <afoias@polymtl.ca>
Date:   Thu Jan 6 15:41:29 2022 -0500

    add sub-56027

 .../sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w_labeled-lesion-manual.nii.gz     |    1 +
 .../labels/sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w_labeled-seg-manual.nii.gz |    1 +
 .../labels/sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w_labels-disc-manual.nii.gz |    1 +
 .../sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w_labeled-lesion-manual.nii.gz |    1 +
 .../labels/sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w_lesion-manual.nii.gz  |    1 +
 .../labels/sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w_seg-manual.nii.gz     |    1 +
 participants.tsv                                                                                        | 3147 ++++++++++++++++++++++++++-------------------------
 sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w.json                                 |   62 +
 sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w.nii.gz                               |    1 +
 sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w.json                             |   63 ++
 sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w.nii.gz                           |    1 +
 11 files changed, 1707 insertions(+), 1573 deletions(-)
(END)
 derivatives/labels/sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labeled-seg-manual.nii.gz        | 1 -
 derivatives/labels/sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w_labeled-lesion-manual.nii.gz | 1 -
 3 files changed, 3 deletions(-)

commit 969354cfb321786bda342843fe624fd9e540b59a
Author: Alexandru Foias <afoias@polymtl.ca>
Date:   Fri Jan 7 11:25:47 2022 -0500

    fix ^M

 participants.tsv | 3146 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++---------------------------------------------------------------------
 1 file changed, 1573 insertions(+), 1573 deletions(-)

commit f2d4de0d43d5d4c99e4ed9833994553b044e1e92
Author: Alexandru Foias <afoias@polymtl.ca>
Date:   Fri Jan 7 10:36:03 2022 -0500

    rename subject

 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labeled-lesion-manual.nii.gz}                                                       | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labeled-seg-manual.nii.gz}                                                          | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w_labels-disc-manual.nii.gz}                                                          | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w_labeled-lesion-manual.nii.gz}                                                   | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w_lesion-manual.nii.gz}                                                           | 0
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w_seg-manual.nii.gz}                                                              | 0
 participants.tsv                                                                                                                                            | 2 +-
 .../anat/sub-56027_ses-20180207_acq-sagcerv_T2w.json => sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w.json       | 2 +-
 .../anat/sub-56027_ses-20180207_acq-sagcerv_T2w.nii.gz => sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcerv_T2w.nii.gz   | 0
 .../sub-56027_ses-20180207_acq-sagcervstir_T2w.json => sub-israelSheba56027/ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w.json    | 2 +-
 .../ses-20180207/anat/sub-israelSheba56027_ses-20180207_acq-sagcervstir_T2w.nii.gz                                                                          | 0
 11 files changed, 3 insertions(+), 3 deletions(-)

commit 38fd2fc3df032546a5cd361fd3a7cf5589e5cf5c
Author: Alexandru Foias <afoias@polymtl.ca>
Date:   Thu Jan 6 15:41:29 2022 -0500

    add sub-56027

 .../sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w_labeled-lesion-manual.nii.gz     |    1 +
 .../labels/sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w_labeled-seg-manual.nii.gz |    1 +
 .../labels/sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w_labels-disc-manual.nii.gz |    1 +
 .../sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w_labeled-lesion-manual.nii.gz |    1 +
 .../labels/sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w_lesion-manual.nii.gz  |    1 +
 .../labels/sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w_seg-manual.nii.gz     |    1 +
 participants.tsv                                                                                        | 3147 ++++++++++++++++++++++++++-------------------------
 sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w.json                                 |   62 +
 sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcerv_T2w.nii.gz                               |    1 +
 sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w.json                             |   63 ++
 sub-56027/ses-20180207/anat/sub-56027_ses-20180207_acq-sagcervstir_T2w.nii.gz                           |    1 +
 11 files changed, 1707 insertions(+), 1573 deletions(-)