data-multi-subject

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Amazon is flakey

1

We've been having sporadic failures due to Amazon rejecting us: https://github.com/spine-generic/data-multi-subject/runs/4226501836?check_suite_focus=true#step:11:711 ``` get derivatives/labels/sub-tokyoSkyra03/anat/sub-tokyoSkyra03_T2star_rms_gmseg-manual.nii.gz (from amazon...) download failed: Internal Server Error Unable to access these remotes: amazon Try making some...

kousu

Upload manual segmentations

11

> ⚠️ This first post is being edited to display the latest strategy/consensus from the team. A derivatives to this dataset was created for the [contrast-agnostic-sofseg](https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord) project. The derived dataset...

jcohenadad

`b0` files are mistakenly filed

6

A bunch of files are tagged `acq-b0` The files affected are all DWI images: ``` u108545@joplin:~/data-multi-subject$ find . -name '*acq-b0*' ./sub-beijingVerio03/dwi/sub-beijingVerio03_acq-b0_dwi.nii.gz ./sub-beijingVerio03/dwi/sub-beijingVerio03_acq-b0_dwi.json ./sub-vallHebron02/dwi/sub-vallHebron02_acq-b0_dwi.nii.gz ./sub-vallHebron02/dwi/sub-vallHebron02_acq-b0_dwi.json ./sub-vallHebron03/dwi/sub-vallHebron03_acq-b0_dwi.nii.gz ./sub-vallHebron03/dwi/sub-vallHebron03_acq-b0_dwi.json ./sub-amu02/dwi/sub-amu02_acq-b0_dwi.nii.gz ./sub-amu02/dwi/sub-amu02_acq-b0_dwi.json ./sub-vallHebron01/dwi/sub-vallHebron01_acq-b0_dwi.json ./sub-vallHebron01/dwi/sub-vallHebron01_acq-b0_dwi.nii.gz...

kousu

jcohenadad

Cannot work out file type of "sub-barcelona01_T1w.nii.gz"

13

I downloaded the images for a few subjects using : `git annex get /sub-oxfordFmrib01/ sub-unf01/ sub-tokyoSkyra01/ sub-stanford01/ sub-milan01/ sub-geneva01/ sub-barcelona01/ sub-hamburg01/ sub-strasbourg01/ sub-tehranS01/` (There is no output when calling this,...

claragiroux

Grant contributors Amazon S3 access for PRs

1

git-annex makes it difficult to use multiple annexes, meaning the fork-and-pull-request model of contribution is awkward: a contributor would need to find their own annex hosting and temporarily add it...

kousu

Eliminate false positives in Checking data consistency

1

alexfoias

Unpaired annotation

1

I noticed that in folder `derivatives/labels/` there exists a group of segmentations `sub-brno0{1:9}` that don't have corresponding images in the main folder. Is this some legacy annotation of are the...

leandervaneekelen

Following on https://github.com/spine-generic/data-multi-subject/issues/36#issuecomment-688535998: Some scans (notably on Philips) might have different signal quantization between the MTon/off and the T1w scan: MT on/off: ~~~ "PhilipsRWVSlope": 1.69499, "PhilipsRWVIntercept": 0, "PhilipsRescaleSlope": 1.69499, ~~~...

jcohenadad

Poor data quality: MT

8

**sub-fslAchieva03_acq-T1w_MTS.nii.gz** **sub-fslAchieva04_acq-T1w_MTS.nii.gz** **sub-fslAchieva05_acq-T1w_MTS.nii.gz** **sub-fslAchieva06_acq-T1w_MTS.nii.gz** **sub-beijingPrisma01_acq-T1w_MTS.nii.gz** **fslAchieva:** Wrong placement (should be centered at C3-C4): --> should remove site from statistics  **sub-balgrist02** Wrong placement  **sub-nottwil03_acq-MToff_MTS.nii.gz**  **sub-nottwil04_acq-MToff_MTS.nii.gz**  **sub-pavia05_acq-MToff_MTS.nii.gz** 

valosekj