Heudiconv Warning: "Unable to determine slice order from CSA tag MosaicRefAcqTimes" on Multi Echo rs-fMRI

, ,
1

Hello everyone!

I am converting our resting state multi echo fMRI data into BIDS format. I have successfully ran heudiconv on the data and converted them to the BIDS format but I had the warning “Unable to determine slice order from CSA tag MosaicRefAcqTimes” which I was wondering how I can manage that.
Furthermore, I was wondering if I have to do anything about “slices not stacked: echo varies (TE 48.22, 30.11; echo 3, 2). Use ‘merge 2D slices’ option to force stacking” and “slices stacked despite varying acquisition numbers (if this is not desired recompile with ‘mySegmentByAcq’)”.

The WARNING:
INFO: stdout 2021-07-29T17:54:59.089696:Warning: Unable to determine slice order from CSA tag MosaicRefAcqTimes
210729-17:54:59,92 nipype.interface INFO:
stdout 2021-07-29T17:54:59.089696:slices not stacked: echo varies (TE 48.22, 30.11; echo 3, 2). Use ‘merge 2D slices’ option to force stacking
INFO: stdout 2021-07-29T17:54:59.089696:slices not stacked: echo varies (TE 48.22, 30.11; echo 3, 2). Use ‘merge 2D slices’ option to force stacking
210729-17:54:59,92 nipype.interface INFO:
stdout 2021-07-29T17:54:59.089696:slices stacked despite varying acquisition numbers (if this is not desired recompile with ‘mySegmentByAcq’)

Thank you very much.
Regards,
Ali

2

what version of dcm2niix? what scanner (Philips/Siemens)? and either any of the Search · Unable to determine slice order from CSA tag MosaicRefAcqTimes · GitHub ring a bell?

3

Sounds like a replication of a previous comment. As noted there, I assume this reflects a high false alarm rate of the current stable release of dcm2niix. These warnings are resolved in the current development branch. So your options are

  1. Ignore, assuming your data was not acquired with Siemens in-built motion correction (moco).
  2. Update your dcm2niix to the development branch.

It is always challenging reverse-engineering proprietary formats like the Siemens CSA header. I have never used Siemens in-built MoCo for my own data as I think it is probably a good idea to have accurate measures of head position as nuisance regressors for subsequent analyses. My handling of the MoCo slice times is a direct translation of the comments I received from Siemens engineers, and I have never validated them. If a user does decide to acquire MoCo data, they should understand this is an edge case where very little validation has been conducted.