Having a look at all the prefiltered_func_data ...
> Hi
>
> On 8 May 2012, at 18:09, Alle Meije Wink wrote:
> > Picking up on an old thread here --
> >
> > I'm trying to run a melodic analysis on the same group in 2 ways.
> > In the first run I do everything as usual, in the second run I want
> > to apply a correction right after motion correction (using the
> > prefiltered_func_data motion parameters).
> >
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0807&L=fsl&P=R19643
> >
> > From this 2008 post I gather that
> > - preprocessing in Feat and in Melodic is identical
> > i.e. is it equivalent to run a full analysis in Melodic, as to do
> > the preprocessings in Feat and then a command-line melodic?
>
> Yes, as far as I remember.
>
> > - there is a way to retrieve the script used by Feat
> > so do the log files produce enough information to reproduce a Feat analysis?
>
> mostly - but there are some calculations in the TCL that won't show up in the log, I'm afraid…….
... would commenting out the line
fsl:exec "/bin/rm -rf prefiltered_func_data"
in featlib.tcl, preserve the files that I need?
I can do the corrections on prefiltered_func_data_mcf I guess, and then continue with the script as mentioned in the log.
Unless there are TCL calculations that don't show up in the log after that?
Or otherwise for just this once, create a featlib.tcl where lines 4966 - 4969
fsl:exec "${FSLDIR}/bin/mcflirt -in $funcdata -out prefiltered_func_data_mcf -mats -plots -refvol $target_vol_number -rmsrel -rmsabs"
if { ! $fmri(regunwarp_yn) } {
set funcdata prefiltered_func_data_mcf
}
are replaced by
fsl:exec "${FSLDIR}/bin/mcflirt -in $funcdata -out prefiltered_func_data_mcf_tmp -mats -plots -refvol $target_vol_number -rmsrel -rmsabs"
fsl:exec "/usr/local/bin/motionproject -in prefiltered_func_data_mcf_tmp -par prefiltered_func_data_mcf.par - out prefiltered_func_data_mcf"
if { ! $fmri(regunwarp_yn) } {
set funcdata prefiltered_func_data_mcf
}
and keep using the Feat GUI -- would that do the trick?
Many thanks!
Best wishes
Alle Meije
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