open-discussion
open-discussion > RE: odd slice timing problem
Nov 17, 2014 03:11 PM | Blaise Frederick
RE: odd slice timing problem
Is this a Siemens scanner? If so, this should be correct. By
the way, looking at your original post, it looks like you didn't
try interleaved ascending in the FSL menu options, which is the
default for most acquisitions on the Trio at least.
In general, for Siemens interleaved acquisitions, if you have an odd number of slices (which you do), you start on slice 1 and do all the odd slices, then all the evens, starting on 2; if you have an even number you do the even slices starting on 2, and then do the odd slices starting on 1 (yes, this is strange, and a source of much confusion). Unless your acquisition is in descending order, in which case you would start at 61 and count down by twos, etc.
The best way to be absolutely sure is to look at the MosaicRefAcqTimes field in the Siemens private dicom header. That will always tell you exactly when each slice was acquired in seconds relative to the start of the TR, starting at the bottom slice. This is especially useful for things like multiband acquisitions where the slice order is extremely difficult to figure out from first principles.
I'm not sure what if any standard tools let you see this field. I have a python script (attached) which digs this out of the header and makes an FSL compatible slice times file (just pipe it into a file).
Blaise
In general, for Siemens interleaved acquisitions, if you have an odd number of slices (which you do), you start on slice 1 and do all the odd slices, then all the evens, starting on 2; if you have an even number you do the even slices starting on 2, and then do the odd slices starting on 1 (yes, this is strange, and a source of much confusion). Unless your acquisition is in descending order, in which case you would start at 61 and count down by twos, etc.
The best way to be absolutely sure is to look at the MosaicRefAcqTimes field in the Siemens private dicom header. That will always tell you exactly when each slice was acquired in seconds relative to the start of the TR, starting at the bottom slice. This is especially useful for things like multiband acquisitions where the slice order is extremely difficult to figure out from first principles.
I'm not sure what if any standard tools let you see this field. I have a python script (attached) which digs this out of the header and makes an FSL compatible slice times file (just pipe it into a file).
Blaise
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Title | Author | Date |
---|---|---|
Chase | Nov 12, 2014 | |
Blaise Frederick | Nov 17, 2014 | |
Chase | Nov 17, 2014 | |
Chase | Nov 17, 2014 | |