to 3d

AFNI Message Board
1

Hello all,

I am working with someone who has collected her data on Siemens Skyra 3T. Her scans are interleaved and oblique.

She found on the to 3d description: Some Siemens .ima files seems to have their EPI slices stored in
spatial order, and some in acquisition (interleaved) order. This
program doesn’t try to figure this out. You can use the command
line option ‘-sinter’ to tell the program to assume that the images
in a single .ima file are interleaved; for example, if there are
7 images in a file, then without -sinter, the program will assume
their order is ‘0 1 2 3 4 5 6’; with -sinter, the program will
assume their order is ‘0 2 4 6 1 3 5’ (here, the number refers
to the slice location in space).

Also for oblıque datasets:
-oblique_origin
assume origin and orientation from oblique transformation matrix
rather than traditional cardinal information (ignores FOV/SLAB
options Sometimes useful for Siemens mosaic flipped datasets

I used the following command to reconstruct a resting state scan:

to3d -prefix ${subject}.REST2_test -save_outliers ${subject}_REST2_test.txt
-time:zt 47 124 3s alt+z /Volumes/HaleDepo/STRESSSPGRREST_150816/${subject}/REST2/M*

I am wondering if this was the wrong way to go? It did seem to pick up that her scans were oblique. I know that “alt+z” indicates that they are interleaved.

Thanks,

Emily

2

Hi Emily,

That notion of interleaved should refer to how the actual
slices are stored in the mosaic. If the EPI volumes look
correct when viewed in afni, then that -sinter option should
not be a worry.

Given that the volumes are now stored correctly on disk,
the alt+z only affects how they are processed during a
3dTshift operation, say, to deal with timing of individual
slices.

Note that you should have the option to use Dimon, e.g.

Dimon -gert_create_dataset -infile_prefix /Volumes/HaleDepo/STRESSSPGRREST_150816/${subject}/REST2/M

From there you could consider options like -dicom_org
and -save_details, if you wanted to.

  • rick
3

Hi Rick,

Sorry to ask you likely this basic question. Is alt+z the same as saying interleaved/alternating Ascending (1,4,2,5,3,6) and alt-z the same as saying interleaved/alternating Descending (6,3,5,2,4,1)?

I am trying to have a better understanding of all of the slice order options in to3d.

From what I understand, Siemens uses Interleaved Ascending 1,4,2,5,3,6 when an odd number of slices are collected. Would “alt+z” be the equivalent to that?

Thanks,

Emily

4

Hi Emily,

That is correct, presumably, though we differ in the
way the ordering is described in 2 ways. We would say
alt+z uses ordering 0,2,4,1,3,5, rather than 1,4,2,5,3,6.
But they are probably just 2 ways of describing the same
thing.

Your 1,4,2,5,3,6 indices probably mean: “for each slice
position, what temporal position does it come from?” So
the first slice was the first acquired, the second slice
was the fourth acquired, etc.

To understand 0,2,4,1,3,5, first note that we index the
slices as offsets, so they just start from 0. Then it
is just the actual order that the slices were acquired,
i.e. first slice 0, then 2, then 4, then 1, 3 and 5.

That is how we will describe them in general, so it is
important to understand the difference.

Anyway, is that clear? Am I correct in the interpretation
of your description the acquisition order?

  • rick
5

Hi Rick,

I have been reading a bit more about Siemens scanners. I believe that for Siemens scanners, if the number of slices collected is odd, you start with the odd slices and if the number of slices is even, you start with the even slices. So the number of slices we collected was odd, I believe we need the order to be 1,3,5,0,2,4. So in this situation, should I use “alt+z2” instead?

Thanks,

Emily

6

Hi Emily,

Yes, that is right (1,3,5,0,2,4,6 is alt+z2).

However, for typical Siemens mosaics, you do not
actually need to specify the slice timing, as Dimon
and to3d will find it in the DICOM headers (and Dimon
tells to3d to use that by specifying the FROM_IMAGE
timing pattern).

So it is likely that you do not need to work so hard
if you use Dimon.

  • rick
7

Hi Rick,

I agree I will plan to use Dimon from now. So, I did use “alt+z” in my to3d command instead of “alt+z2”. So, I am assuming this will screw up slice timing correction in afni proc py?

Emily

8

Yes, it would certainly be good to fix that.

Using alt+z vs alt+z2 would throw of both the odd
and even slices by 1/2 TR in opposite directions.
So the net difference would put their times a full
TR off between each other.

You might go back to start with Dimon now, or
maybe use FROM_IMAGE timing directly in to3d,
just to be sure.

  • rick
9

Hi Rick,

I am attempting to use Dimon, but am running into some errors.

My script is:

#!/bin/tcsh

foreach subject (AGS)

Dimon -infile_prefix ‘/Volumes/Emily/${subject}/REST1/*.dcm’ -gert_create_dataset -save_details ${subject}_dcm

end

I get the following error: error: invalid option </Users/emilybelleau/Documents/AGS/REST1/IM-0001-0002-0001.dcm>

Any thoughts on what could be going on?

Thanks,

Emily

10

Hi Emily,

I am going to guess it is a combination of having a
link in there (/Volumes/Emily points to the Documents
directory) and the quotes not being correct, since
Dimon is complaining about one of the input files.

Be sure the -infile_prefix parameter is surrounded by
typical single quotes.

If you cannot get that to work, please send me the
actual script via email.

  • rick
11

Hi Rick,

I am actually getting an “operation not permitted” error when I try to run Dimon. Any ideas why this could be going on and how to solve?

Thanks,
Emily

12

Hi Emily,

Would you please send me email with:

  1. Your Dimon command or script.
  2. The complete screen text from running it.
  3. The output of running “ls -l” in that directory.

Click on my name for my email address.

Thanks,

  • rick