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spinal-cord-7t / coil-qc-code

7T Spinal Cord Coil QC Analysis Code
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`sub-MPI2_inv-1_part-mag_MP2RAGE.nii.gz` is missing #48

Closed jcohenadad closed 2 months ago

jcohenadad commented 2 months ago

This image is missing from https://doi.org/10.18112/openneuro.ds005025.v2.2.0

We need it for #47

Any reason for this? @evaalonsoortiz @Kyota-exe

Kyota-exe commented 2 months ago

Only the UNI images MP2RAGE scan was acquired for subject2 of MPI. This is the case for CRMBM as well. I asked @evaalonsoortiz about this in the past, and she said that it was fine because we only use the UNI images scan for the analysis, but now that this is no longer the case, I'm not sure what the original reason is for why they are missing.

evaalonsoortiz commented 2 months ago

I'll reach out to our contacts at MPI and CRMBM to see if we can get the sub-xxx_inv-1_part-mag_MP2RAGE.nii.gz scans.

Kyota-exe commented 2 months ago

@evaalonsoortiz Note that only subject2 is lacking those scans; the other subjects have them.

evaalonsoortiz commented 2 months ago

Subject2 for both sites? What name does subject2 correspond to? D, R, or L?

Kyota-exe commented 2 months ago

Yes, subject2 for both sites, which corresponds to L.

I’m not sure we still need them for the analysis, however; @jcohenadad has already resolved #47 with a manual segmentation for sub-MPI2.

jcohenadad commented 2 months ago

I'll reach out to our contacts at MPI and CRMBM to see if we can get the sub-xxx_inv-1_part-mag_MP2RAGE.nii.gz scans.

I would also ask for inv-2 (just in case...)

I’m not sure we still need them for the analysis, however; @jcohenadad has already resolved https://github.com/spinal-cord-7t/coil-qc-code/issues/47 with a manual segmentation for sub-MPI2.

Better to be exhaustive and consistent across subjects, regardless the analysis pipeline

evaalonsoortiz commented 2 months ago

Emails have been sent, I'll share the data with @Kyota-exe when I get them.

evaalonsoortiz commented 2 months ago

Update: inv-1 and inv-2 scans for CRMBM have been added to our internal servers and sent to @Kyota-exe for uploading to openneuro

Kyota-exe commented 2 months ago

The INV1 and INV2 scans for CRMBM have been uploaded to the dataset: https://openneuro.org/datasets/ds005025

evaalonsoortiz commented 2 months ago

Update: inv-1 and inv-2 scans for sub-MPI2 have been added to our internal servers and sent to @Kyota-exe for uploading to openneuro

Kyota-exe commented 2 months ago

The MP2RAGE INV1 and INV2 scans for sub-MPI2 have been uploaded to OpenNeuro in v2.4.0. This issue should now be resolved.