Dear FSL People,
Could you please clarify the situation a bit for me and correct me where
I am wrong.
Looking at feat.tcl and report.log I got an impression (please
correct me if I am wrong), that
1. mcflirt takes middle of the sequence as the reference image, and it
doesn't care about optional parameter such as alternative_example_func
and there is no parameter to provide alternative 'target_vol_number':
,---------------------------------------------------
| set target_vol_number [ expr $total_volumes / 2 ]
`---
2. example_func (which is used later on for registration) is extracted
prior the run of mcflirt, and by default (unless
alternative_example_func is provided) the very first volume is taken to
be the reference
,-----------------------------------------------------------------------------
| fsl:exec "${FSLDIR}/bin/avwroi $funcdata example_func $target_vol_number 1"
`---
3. mcflirt is ran (so now example_func is not really an example of real
data)
The problem I see is that if there is considerable motion between 1st
and 'middle' volume, all the registration of the results is skewed,
because statistics are computed on motion corrected data taking middle
volume as the reference; and registration is based on the 1st volume
prior to motion correction.
Having an option to specify which volume to use for motion correction is
very beneficial imho especially if field correction is used and most
probably field mapping happens right after BOLD sequence, so that field
map and BOLD as aligned correctly. In such cases, I guess, taking the
last volume as the reference for mcflirt and registration should be the
right thing to do.
--
.-.
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