MS data from Dresden

[plbenveniste]

In this issue, I discuss the steps taken to Git-Annex the data from Dresden.
(email: MP2RAGE Dresden data, date: 2025-10-13)

[plbenveniste]

What should be the dataset name ? @jcohenadad ms-dresden-mp2rage ? Or ms-dresden-2025 ?

[plbenveniste]

Data was downloaded and saved to duke/temp/plben/ms-lesion-agnostic/data_dresden/MSMyelon3D_mp2rage

[jcohenadad]

how about ms-dresden-mp2rage-2025?

[plbenveniste]

how about ms-dresden-mp2rage-2025?

Sure!
@mguaypaq could you create the git-annex repo please?

[mguaypaq]

Done, and I gave @plbenveniste write access:
https://data.neuro.polymtl.ca/datasets/ms-dresden-mp2rage-2025

[plbenveniste]

Thanks!

[plbenveniste]

Here is an example subject.

(base) p119007@GRAMES.POLYMTL.CA@romane:~/create_dresden_data/MSMyelon3D_mp2rage/sub-SPINE010$ tree
.
├── ses-0m
│   └── anat
│       ├── sub-SPINE010_ses-0m_acq-STIR_run-01_T2w.json
│       ├── sub-SPINE010_ses-0m_acq-STIR_run-01_T2w.nii.gz
│       ├── sub-SPINE010_ses-0m_acq-STIR_run-02_T2w.json
│       ├── sub-SPINE010_ses-0m_acq-STIR_run-02_T2w.nii.gz
│       ├── sub-SPINE010_ses-0m_acq-STIR_run-03_T2w.json
│       └── sub-SPINE010_ses-0m_acq-STIR_run-03_T2w.nii.gz
└── ses-12m
    └── anat
        ├── sub-SPINE010_ses-12m_acq-STIR_run-01_T2w.json
        ├── sub-SPINE010_ses-12m_acq-STIR_run-01_T2w.nii.gz
        ├── sub-SPINE010_ses-12m_acq-STIR_run-02_T2w.json
        ├── sub-SPINE010_ses-12m_acq-STIR_run-02_T2w.nii.gz
        ├── sub-SPINE010_ses-12m_acq-STIR_run-03_T2w.json
        ├── sub-SPINE010_ses-12m_acq-STIR_run-03_T2w.nii.gz
        ├── sub-SPINE010_ses-12m_acq-STIR_run-04_T2w.json
        ├── sub-SPINE010_ses-12m_acq-STIR_run-04_T2w.nii.gz
        ├── sub-SPINE010_ses-12m_run-01_inv-1_MP2RAGE.bval
        ├── sub-SPINE010_ses-12m_run-01_inv-1_MP2RAGE.bvec
        ├── sub-SPINE010_ses-12m_run-01_inv-1_MP2RAGE.json
        ├── sub-SPINE010_ses-12m_run-01_inv-1_MP2RAGE.nii.gz
        ├── sub-SPINE010_ses-12m_run-01_inv-2_MP2RAGE.bval
        ├── sub-SPINE010_ses-12m_run-01_inv-2_MP2RAGE.bvec
        ├── sub-SPINE010_ses-12m_run-01_inv-2_MP2RAGE.json
        ├── sub-SPINE010_ses-12m_run-01_inv-2_MP2RAGE.nii.gz
        ├── sub-SPINE010_ses-12m_run-01_T1MAP.json
        ├── sub-SPINE010_ses-12m_run-01_T1MAP.nii.gz
        ├── sub-SPINE010_ses-12m_run-01_UNIT1.json
        ├── sub-SPINE010_ses-12m_run-01_UNIT1.nii.gz
        ├── sub-SPINE010_ses-12m_run-02_inv-1_MP2RAGE.bval
        ├── sub-SPINE010_ses-12m_run-02_inv-1_MP2RAGE.bvec
        ├── sub-SPINE010_ses-12m_run-02_inv-1_MP2RAGE.json
        ├── sub-SPINE010_ses-12m_run-02_inv-1_MP2RAGE.nii.gz
        ├── sub-SPINE010_ses-12m_run-02_inv-2_MP2RAGE.bval
        ├── sub-SPINE010_ses-12m_run-02_inv-2_MP2RAGE.bvec
        ├── sub-SPINE010_ses-12m_run-02_inv-2_MP2RAGE.json
        ├── sub-SPINE010_ses-12m_run-02_inv-2_MP2RAGE.nii.gz
        ├── sub-SPINE010_ses-12m_run-02_T1MAP.json
        ├── sub-SPINE010_ses-12m_run-02_T1MAP.nii.gz
        ├── sub-SPINE010_ses-12m_run-02_UNIT1.json
        ├── sub-SPINE010_ses-12m_run-02_UNIT1.nii.gz
        ├── sub-SPINE010_ses-12m_run-03_inv-2_MP2RAGE.bval
        ├── sub-SPINE010_ses-12m_run-03_inv-2_MP2RAGE.bvec
        ├── sub-SPINE010_ses-12m_run-03_inv-2_MP2RAGE.json
        ├── sub-SPINE010_ses-12m_run-03_inv-2_MP2RAGE.nii.gz
        ├── sub-SPINE010_ses-12m_run-03_UNIT1.json
        ├── sub-SPINE010_ses-12m_run-03_UNIT1.nii.gz
        ├── sub-SPINE010_ses-12m_run-04_inv-2_MP2RAGE.bval
        ├── sub-SPINE010_ses-12m_run-04_inv-2_MP2RAGE.bvec
        ├── sub-SPINE010_ses-12m_run-04_inv-2_MP2RAGE.json
        ├── sub-SPINE010_ses-12m_run-04_inv-2_MP2RAGE.nii.gz
        ├── sub-SPINE010_ses-12m_run-04_UNIT1.json
        └── sub-SPINE010_ses-12m_run-04_UNIT1.nii.gz

5 directories, 50 files

I am surprised to see bval and bvec files for MP2RAGE images, which, in my understanding, are normally associated with DWI images. What should I do with those files? @jcohenadad

[jcohenadad]

I am surprised to see bval and bvec files for MP2RAGE images, which, in my understanding, are normally associated with DWI images. What should I do with those files?

I'm also quite surprised. Maybe it's a DCM2BIDS glitch. I suggest we just keep them, just in case...

[plbenveniste]

I'm also quite surprised. Maybe it's a DCM2BIDS glitch. I suggest we just keep them, just in case...

Okay, will do! I will add those files to the sourcedata folder so that they are not lost and at the same time they are not in the curated data.

[plbenveniste]

I have bidsified the data.

The only issue I am faced with is this one:

(base) p119007@GRAMES.POLYMTL.CA@romane:~/create_dresden_data/ms-dresden-mp2rage-2025$ bids-validator .
bids-validator@1.9.7
bids-specification@disable
(node:1625424) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
	1: [ERR] sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation. (code: 60 - SFORM_AND_QFORM_IN_IMAGE_HEADER_ARE_ZERO)
		./sub-SPINE046/ses-M0/anat/sub-SPINE046_ses-M0_acq-STIR_run-08_T2w.nii.gz
		./sub-SPINE046/ses-M0/anat/sub-SPINE046_ses-M0_acq-STIR_run-11_T2w.nii.gz
		./sub-SPINE092/ses-M0/anat/sub-SPINE092_ses-M0_run-01_T1map.nii.gz
		./sub-SPINE092/ses-M0/anat/sub-SPINE092_ses-M0_run-03_T1map.nii.gz
		./sub-SPINE093/ses-M0/anat/sub-SPINE093_ses-M0_run-02_T1map.nii.gz
		./sub-SPINE093/ses-M0/anat/sub-SPINE093_ses-M0_run-03_T1map.nii.gz
		./sub-SPINE094/ses-M0/anat/sub-SPINE094_ses-M0_run-01_T1map.nii.gz
		./sub-SPINE094/ses-M0/anat/sub-SPINE094_ses-M0_run-03_T1map.nii.gz
		./sub-SPINE099/ses-M0/anat/sub-SPINE099_ses-M0_run-02_T1map.nii.gz
		./sub-SPINE099/ses-M0/anat/sub-SPINE099_ses-M0_run-04_T1map.nii.gz
		... and 27 more files having this issue (Use --verbose to see them all).

@mguaypaq How should I deal with this? Should I just include these images to an exclude file?
@jcohenadad We should maybe mention this issue to Hagen and his team ? Maybe at the same time, we could mention the bval and bvec issue ?

[mguaypaq]

After looking at one of the nifti headers in your error message, it looks like the qform and sform are almost default/fallback values. Also, they don't match each other: the qform uses the voxel resolution from the pixdim field (not isotropic), and the sform uses a 1x1x1 voxel resolution.

You could use sct_image -set-sform-to-qform to at least copy the voxel resolution from the qform to the sform. But I wouldn't trust the image orientation without actually looking at the images, and even then you couldn't really be sure about the left-right axis. Also, you couldn't assume that different images of the same subject are correctly translated in space (for example, if you want to do stitching).

So, these 37 images are maybe only usable with a lot of caution.

Also, when I ran bids-validator, it complained about some missing required fields in the JSON sidecars for 277 MP2RAGE images:

• RepetitionTimeExcitation
• RepetitionTimePreparation
• NumberShots

But I'm guessing it would be impossible for you to actually get those values now, in which case we can ignore this.

[plbenveniste]

Thanks for the thorough answer, Mathieu! I will run sct_image -set-sform-to-qform for each image and will open each in fsleyes to assert that the orientation is correct.
Should we create an exclude.yml file to mention this issue? What is your opinion?

Full lists of images:

        ./sub-SPINE046/ses-M0/anat/sub-SPINE046_ses-M0_acq-STIR_run-08_T2w.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE046/ses-M0/anat/sub-SPINE046_ses-M0_acq-STIR_run-11_T2w.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE092/ses-M0/anat/sub-SPINE092_ses-M0_run-01_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE092/ses-M0/anat/sub-SPINE092_ses-M0_run-03_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE093/ses-M0/anat/sub-SPINE093_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE093/ses-M0/anat/sub-SPINE093_ses-M0_run-03_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE094/ses-M0/anat/sub-SPINE094_ses-M0_run-01_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE094/ses-M0/anat/sub-SPINE094_ses-M0_run-03_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE099/ses-M0/anat/sub-SPINE099_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE099/ses-M0/anat/sub-SPINE099_ses-M0_run-04_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE102/ses-M0/anat/sub-SPINE102_ses-M0_run-01_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE102/ses-M0/anat/sub-SPINE102_ses-M0_run-03_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE103/ses-M0/anat/sub-SPINE103_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE104/ses-M0/anat/sub-SPINE104_ses-M0_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE105/ses-M0/anat/sub-SPINE105_ses-M0_acq-STIR_run-03_T2w.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE105/ses-M0/anat/sub-SPINE105_ses-M0_acq-STIR_run-05_T2w.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE105/ses-M0/anat/sub-SPINE105_ses-M0_acq-STIR_run-06_T2w.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE105/ses-M0/anat/sub-SPINE105_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE105/ses-M0/anat/sub-SPINE105_ses-M0_run-03_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE108/ses-M0/anat/sub-SPINE108_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE108/ses-M0/anat/sub-SPINE108_ses-M0_run-04_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE108/ses-M0/anat/sub-SPINE108_ses-M0_run-05_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE113/ses-M0/anat/sub-SPINE113_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE113/ses-M0/anat/sub-SPINE113_ses-M0_run-04_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE122/ses-M0/anat/sub-SPINE122_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE122/ses-M0/anat/sub-SPINE122_ses-M0_run-04_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE126/ses-M0/anat/sub-SPINE126_ses-M0_run-01_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE126/ses-M0/anat/sub-SPINE126_ses-M0_run-03_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE129/ses-M0/anat/sub-SPINE129_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE131/ses-M0/anat/sub-SPINE131_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE132/ses-M0/anat/sub-SPINE132_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE133/ses-M0/anat/sub-SPINE133_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE134/ses-M0/anat/sub-SPINE134_ses-M0_run-01_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE135/ses-M0/anat/sub-SPINE135_ses-M0_run-01_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE136/ses-M0/anat/sub-SPINE136_ses-M0_run-02_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE139/ses-M0/anat/sub-SPINE139_ses-M0_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.
		./sub-SPINE142/ses-M0/anat/sub-SPINE142_ses-M0_T1map.nii.gz
			sform_code and qform_code in the image header are 0. The image/file will be considered invalid or assumed to be in LAS orientation.

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