indi > CORRECTION RE: Acquisition order
Apr 1, 2011  07:04 PM | Xiaozhen You
CORRECTION RE: Acquisition order
Dear Michael,
I'm still not sure about the slice timing after reading the threads. 
So for NYU, the slice number is 33 (as I load it in FSL and SPM).
So should the slice timing order be [1 3 ... 33 2 4 ... 32] for NYU interleaved acending sequence?
Thanks!
Best,
Xiaozhen
Originally posted by Michael Milham:
Dear Pierre,

Based upon your feedback, we had our physicist revisit the issue of slice timing for the protocol.

You are correct, the acquisition order is INTERLEAVED, ASCENDING.

With respect to first acquisition slice, that is EVEN (slice 2, with indexing starting at 1), as the # of slices is an even number.

Many thanks for bringing this inaccuracy to our attention - I apologize for any inconveniences this error may have caused anyone.

Best,
Mike



Originally posted by Pierre Bellec:
Dear Michael,

Unfortunately, I am now confused about the slice timing altogether. My basic understanding is that an interleaved acquisition is, by default, ascending (from foot to head, F->H) with odd slices first. The Siemens scanner have a different convention, in that if the number of slices is odd, it starts by odd slices, and if the number of slices is even, it starts by even slices. Anyway, I don't think slice timing correction has much of an impact on slow temporal fluctuations, but with the current infos found in the release table (which is missing the scanner type) it may not be possible to get the slice timing right.

As a side comment, one also has to take into consideration how the volume is stored. Depending on the software you are using, slice timing correction is usually applied in the voxel space. So if the acquisition was F->H (ascending), but the first slice in the volume is on the H side, this needs to be coded as a descending scheme ... I wish there were a reliable way to derive slice timing information ...

Best regards,

Pierre[/userquote]

Threaded View

TitleAuthorDate
Michel Grothe Nov 24, 2010
Pierre Bellec Nov 29, 2010
Michael Milham Nov 30, 2010
Maarten Mennes Aug 2, 2011
Arno Klein May 26, 2011
Clare Kelly May 27, 2011
CORRECTION RE: Acquisition order
Xiaozhen You Apr 1, 2011
Michael Milham Nov 24, 2010
Michel Grothe Nov 25, 2010
Michael Milham Nov 28, 2010