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Repo that deals with datalad aspects for internal use
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Adding 7T MP2RAGE data from Leipzig #322

Closed jcohenadad closed 6 days ago

jcohenadad commented 2 weeks ago

Contact: Falk Eippert suggestion for name: leipzig-7t-mprage hc-leipzig-7t-mp2rage

valosek@macbook-pro:~/Downloads/MP2RAGE_2share$ tree
.
├── sub-sspr17
│   ├── anat.nii.gz
│   └── anat_crop_biascorr_denoise.nii.gz
├── sub-sspr18
│   ├── anat.nii.gz
│   └── anat_crop_biascorr_denoise.nii.gz
├── sub-sspr19
│   ├── anat.nii.gz
│   └── anat_crop_biascorr_denoise.nii.gz
├── sub-sspr20
│   ├── anat.nii.gz
│   └── anat_crop_biascorr_denoise.nii.gz
├── sub-sspr21
│   ├── anat.nii.gz
│   └── anat_crop_biascorr_denoise.nii.gz
...
valosekj commented 2 weeks ago

Do we want to put anat_crop_biascorr_denoise images to the root directory or to derivatives?

root:

.
├── dataset_description.json
├── participants.tsv
├── sub-sspr17
│   └── anat
│       ├── sub-sspr17_inv-2_MP2RAGE.nii.gz
│       └── sub-sspr17_desc-crop_biascorr_denoise_inv-2_MP2RAGE.nii.gz
├── sub-sspr18
│   └── anat
│       ├── sub-sspr18_inv-2_MP2RAGE.nii.gz
│       └── sub-sspr18_desc-crop_biascorr_denoise_inv-2_MP2RAGE.nii.gz
...

derivatives:

.
├── dataset_description.json
├── participants.tsv
├── sub-sspr17
│   └── anat
│       └── sub-sspr17_inv-2_MP2RAGE.nii.gz
├── sub-sspr18
│   └── anat
│       └── sub-sspr18_inv-2_MP2RAGE.nii.gz
...
└── derivatives
    └── preprocessing
        ├── sub-sspr17
        │   └── anat
        │       └── sub-sspr17_desc-crop_biascorr_denoise_inv-2_MP2RAGE.nii.gz
        ├── sub-sspr18
        │   └── anat
        │       └── sub-sspr18_desc-crop_biascorr_denoise_inv-2_MP2RAGE.nii.gz
...

(I'm using inv-2_MP2RAGE based on https://github.com/ivadomed/model-spinal-rootlets/issues/45) (Useful resource: MP2RAGE bids-example)

jcohenadad commented 2 weeks ago

I'm using inv-2_MP2RAGE based on https://github.com/ivadomed/model-spinal-rootlets/issues/45

excellent

We should also ask for the first inversion, and the reconstructed UNI data. If we do get the UNI data, we should call this dataset mp2rage-- if not, let's keep mprage

valosekj commented 2 weeks ago

Meanwhile, @mguaypaq, could you please initialize a new dataset (leipzig-7t-mprage leipzig-7t-mp2rage) and add me as a collaborator? Thanks!

mguaypaq commented 2 weeks ago

@nullnik-0 do you want to do it? It would be a good occasion to test the new admin instructions. Feel free to ping me on slack if anything is unclear.

valosekj commented 1 week ago

We should also ask for the first inversion, and the reconstructed UNI data. If we do get the UNI data, we should call this dataset mp2rage-- if not, let's keep mprage

👍🏻

@NathanMolinier, just FYI, we now have the following three images for each subject:

- sub-sspr17/sub-sspr17_acq-ND_inv-1_MP2RAGE.nii.gz
- sub-sspr17/sub-sspr17_acq-ND_inv-2_MP2RAGE.nii.gz
- sub-sspr17/sub-sspr17_acq-ND_UNI.nii.gz
NathanMolinier commented 1 week ago

@NathanMolinier, just FYI, we now have the following three images for each subject:

Seems good to me !

Update: For records, we used _UNIT1 instead of _UNI to be bids compliant

NathanMolinier commented 1 week ago

We should also ask for the first inversion, and the reconstructed UNI data. If we do get the UNI data, we should call this dataset mp2rage

Should we rename this dataset leipzig-7t-mp2rage ? As mentioned by @jcohenadad

valosekj commented 1 week ago

We should also ask for the first inversion, and the reconstructed UNI data. If we do get the UNI data, we should call this dataset mp2rage

Should we rename this dataset leipzig-7t-mp2rage ? As mentioned by @jcohenadad

Yes! The images are MP2RAGE.

NathanMolinier commented 1 week ago

Regarding subject naming (sub-sspr17) do we want to use zero padding (sub-sspr017) is case we receive more data ? But even though, according to bids, it is not mandatory.

Update: maybe we can keep the names without padding and update if we receive more data

NathanMolinier commented 1 week ago

@nullnik-0 could you initialize the dataset hc-leipzig-7t-mp2rage and grant me writing access ? Thank you

jcohenadad commented 1 week ago

Update: maybe we can keep the names without padding and update if we receive more data

yes-- i don't think we will receive more data (or at least no more than 100)

nullnik-0 commented 6 days ago

@nullnik-0 could you initialize the dataset hc-leipzig-7t-mp2rage and grant me writing access ?

Apologies for the delay. The dataset has been initialized and is accessible here. @valosekj and @NathanMolinier should both have write access. Let me know if there are any issues.