Niifti conversion to BIDS?

[Steven]

Hi @ShuningW,

If the required metadata described above are consistent across the subjects with metadata available, then it is probably safe to use the same. As mentioned earlier you can place the json in the BIDS root and it will be inherited for everyone.

Best,
Steven

[abore]

Dear @ajschadler,

If you still looking for a software to sort your nifti+json into a bids structure.
Dcm2bids can be your solution. Dcm2bids can skip the dcm2niix conversion and just organize your nifti+json into BIDS structure.

Don’t hesitate if you have any questions.

Best,
Arnaud

[ShuningW]

Hi,

I have two questions regarding fMRIPrep.

First, I have about 90 participants, but 6 of them do not have DICOM data, which means I cannot obtain their slice timing data. This results in the ability to perform slice timing correction for the other participants, but not for these 6. Should I exclude these 6 participants entirely, or is it acceptable for them to proceed without slice timing correction while the others undergo it?

Second, similarly, out of the 90 participants, 30 do not have T2-weighted data. Should I use the T2w data for the participants who have it and simply omit T2w for those who do not, or should I uniformly avoid using T2w data for all participants?

Thank you very much!

Bests,
Shuning

[Steven]

Hi @ShuningW,

For future reference, separate questions should be submitted as different issues.

@ShuningW

First, I have about 90 participants, but 6 of them do not have DICOM data, which means I cannot obtain their slice timing data.

If the same protocol was used across participants, slice timing should be the same.

@ShuningW

Should I exclude these 6 participants entirely, or is it acceptable for them to proceed without slice timing correction while the others undergo it?

You should apply (or not apply) slice timing uniformly across participants.

@ShuningW

Second, similarly, out of the 90 participants, 30 do not have T2-weighted data. Should I use the T2w data for the participants who have it and simply omit T2w for those who do not, or should I uniformly avoid using T2w data for all participants?

It is only used for refining the pial surface in FreeSurfer, so it should have negligible, if any, effect on your fmri results. I would just use it when available.

Best,
Steven

[ShuningW]

hi @Steven,

Thank you very much for your response! I apologize for not separating the different questions this time.

Regarding the first question about slice timing, my participants have the same scanning protocol, but there are slight differences in their slice timing, as shown in the screenshot below. This is the slice timing for the same run from different participants; while most of the timings are the same, there are two slices with slight variations.

[Steven]

Given the slow nature of BOLD signals, I would’t worry time deviations this small.

[ajschadler]

For my own curiosity, is the correspondence between (0018,0024) SequenceName and modality-type generally consistent within vendors?