Adding 7T MP2RAGE data from Leipzig

[jcohenadad]

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]

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 ivadomed/model-spinal-rootlets#45)
(Useful resource: MP2RAGE bids-example)

[jcohenadad]

I'm using inv-2_MP2RAGE based on ivadomed/model-spinal-rootlets#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]

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

[mguaypaq]

@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]

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]

@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]

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]

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]

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]

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

[jcohenadad]

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]

@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.