OK, thanks! I also just realized I could hardcode it into fsl_motion_outliers by editing the call to mcflirt:
$FSLDIR/bin/mcflirt -in $mcf -out ${outdir}_mc/fmri_mcf -mats -plots -refvol $refnum -rmsrel -rmsabs
Sorry I didn't look at this before posting.
Cheers,
David
On Dec 16, 2014, at 6:44 PM, Mark Jenkinson <[log in to unmask]> wrote:
> Hi,
>
> I’m afraid this isn’t an option at the moment, but this is something we will look at adding in future versions.
>
> All the best,
> Mark
>
>
>> On 5 Dec 2014, at 03:16, David V. Smith <[log in to unmask]> wrote:
>>
>> Hello,
>>
>> It looks like fsl_motion_outliers defaults to the middle volume as the reference scan for some metrics (e.g., fdrms). Is there any way to specific a different volume as the reference scan? I’m opting to use the first volume as the reference scan during motion correction, so I’d like to be consistent in fsl_motion_outliers.
>>
>> Thanks!
>> David
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