Dear Manuel,
> Dear FSL experts,
>
> I'm interested to use the mporder option in eddy, as I'm working in infant population I expect the data to have huge motion.
>
> I found in the wiki: "If one wants to do slice-to-vol motion correction --mporder should be set to an integer value greater than 0 and less than the number of excitations in a volume". Probably is a naiv question, but how I can found the number of excitations in a volume from my dataset ? In the provided example the selected values is 6, I don't know if this is correct for all datasets.
for most data the number of excitations (per volume) is the same as the number of slices. It is only for multi-band acquisitions (also known as SMS) that they are different. In those cases you acquire more than one slice per excitation. For example an MB/SMS factor of 3 means that you acquired 3 slices for each excitation. If you for example have 63 slices and an MB/SMS factor of 3 it means that you have 21 excitations.
I don’t really have a hard and fast rule for the --mporder factor. The slice-to-vol is time consuming, so based on that you might want to use a “reasonable” value. If you for example have a “regular” sequence with 64 slices (and hence 64 excitations) I would not recommend going higher than 64/4=16
>
> Another question: for the --mporder option is needed the --slspec file, when this file is included, in the --repol configuration, is there a need to add the --mb or --mb_offs if I'm using the --ol_type=both?
No, the --slspec file supersedes the --mb and --mb_offs parameters. The latter are still supported (as long as you don’t also specify --slspec), but I am considering to have them phased out in future releases.
> and because I'm working with infants, with small head sizes, is advised to modife the default value of --ol_nvox? Thanks in advance.
No, I would be careful with that. The reason --ol_nvox is there is to ensure that when we assess if a slice is an outlier there are enough voxels with potential signal in them to be able to determine that.If one sets it too low I fear that one would start to get false positives (i.e. one discards slices that aren’t really outliers).
Jesper
>
> Regards,
>
> Manuel
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