Hello,

We collected a multimodal imaging dataset using a Siemens Magnetom (prisma_fit) scanner. I used dcm2niix version v1.0.20210317 to convert the data to nifti format. During the conversion step, I am getting several warnings. Specifically, the warning during conversion of the functional data is "Warning: Adjusting for negative MosaicRefAcqTimes (issue 271)". According to our acquisition protocol, motion correction was off for the functional scan. The resulting image looks ok and the TR/TE in the .json file matches acquisition parameters. I saw in previous posts this is likely a false alarm but wanted to get your input. 

I get the same negative MosaicRefAcqTimes (issue 271) warning for the conversion of DTI data and a high resolution T2-weighted scan of the hippocampus. Additionally, we get the warning "Warning: interpolated protocol 'anat' may be unsuitable for dwidenoise/mrdegibbs' when converting the FLAIR and neuromelanin scans. Again, the resulting images look ok. Is this a cause for concern?

Thanks in advance!
Jenna

I would look at issue 271:
  https://github.com/rordenlab/dcm2niix/issues/271
Specifically:

Just a comment that the current stable release (v1.0.20210317) will often generate false alarms that refer to this issue: Adjusting for negative MosaicRefAcqTimes (issue 271). This is resolved in the development branch and will be fixed in the Fall 2021 stable release.

Ok, thank you! Additionally, we get the warning "Warning: interpolated protocol 'anat' may be unsuitable for dwidenoise/mrdegibbs' when converting the FLAIR and neuromelanin scans to nifti. Again, the resulting images look ok. Is this a cause for concern?

Thanks,
Jenna

1. In general, data that are interpolated in plane require x4 the disk space, process slower, and are unsuitable for tools like mrdegibbs. Unless you use that tool, you can probably ignore this message. However, if possible I would turn off interpolation for all future acquisitions.
  https://mrtrix.readthedocs.io/en/latest/reference/commands/mrdegibbs.html


2. I notice you also had some issues with repetition time. Were these resolved, or are there still issues? Feel free to send me a link to the DICOMs (e.g. email a link to GoogleDrive archive) if you are still having issues
  https://afni.nimh.nih.gov/afni/community/board/read.php?1,166894,166919#msg-166919

Hi Chris,

Thanks for your response. Yes, I am still having issues with repetition time. Where should I email the GoogleDrive link to?

Thanks,
Jenna

Originally posted by Chris Rorden:

The user name in this message board is a link. Click on this for the email address of the user.

I can confirm that the Philips data you sent me contains conflicting information regarding the repetition time. The issue is described here:

  https://github.com/rordenlab/dcm2niix/issues/560