Should I use tshift for multiband sequence?

AFNI Message Board
1

Hi,

I’m using sms_mghS3G2 sequence for my experiment. In to3d I put alt+z as tpattern. It said that tshift will take tpattern information from header files which I believe should be what I put in. But I don’t know whether this is correct for my multiband sequence.

I know that this sequence start from the bottom of the brain and can take multiple slices at the same time. My question is whether alt+z could capture the real sequence order.

Thanks!
Lingyan

2

Alt-z may not be appropriate. The best approach is to check with your scanner group or to read in the info using Dimon, which will output the slice information from the headers. You can then specify those timings into a file and use the @filename option of 3dTshift (or afni_proc.py).

3

Hi Lingyan,

As Peter suggested, do not use alt+z for the tpattern in a
multiband sequence. None of the pre-defined timing
patterns are appropriate for multiband timing, which has
multiple slices being acquired at the same time.

Are you using a Siemens scanner? If so, it should be
easy to get the times from the header. If not, you may
have to get them elsewhere.

Also, how long are the stimulus events?

  • rick
4

Hi Rick and Peter,

Thanks. Yes I’ am using a Siemens prisma scanner. I thought the timing order in header files is the alt+z we put in to3d when creating it?

I used a block deign. My stimulus events are about 12s long and TR is 1.5s. I’ve used tshift in my previous analysis, hopefully it will not make a big difference.

Lingyan

5

Hi Lingyan,

Are you using “Dimon -gert_create_dataset …” to make the datasets?
If so, it would probably specify the slice timing as FROM_IMAGE, which
would have to3d extract the slice times from the Dicom files.

You can use dicom_hdr -slice_times to show the slice timing in
the original Dicom files, assuming they are correctly populated.

  • rick
6

Hi Rick,

Thanks a lot! I tried with dimon and it works very well – the timing matches with dicom_hdr slice timing information. I’ve verified that using to3d directly with alt+z didn’t give the correct slice timing.

Lingyan