fMRIVolume OneStepResampling.sh is breaking the TR if input data is not in seconds

[cmpetty]

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When data is passed to OneStepResampling.sh that has TR in ms it is breaking the files afterwards because the time_units are not being accounted for.

You're saving the TR, then re-setting in later with fslmerge, but fslmerge requires TR in seconds.

We found that our files after this step had TR set to 1000.00 seconds, instead of 1 sc, or 1000.00 ms

I added some code to account for different units and adjust before it got to the fslmerge step

##Save TR for later
TR_vol=`${FSLDIR}/bin/fslval ${InputfMRI} pixdim4 | cut -d " " -f 1`
TR_units=`${FSLDIR}/bin/fslval ${InputfMRI} time_units | cut -d " " -f 1`
NumFrames=`${FSLDIR}/bin/fslval ${InputfMRI} dim4`

##added to account for time units
if [ ${TR_units} = "s" ] ; then
        # this is fine
        continue
elif [ ${TR_units} = "ms" ] ; then 
        TR_vol=$( perl -e "print $TR_vol / 1000.0");
elif [ ${TR_units} = "us" ] ; then
        TR_vol=$( perl -e "print $TR_vol / 1000000.0");
fi

##Merge together results and restore the TR (saved beforehand)
${FSLDIR}/bin/fslmerge -tr ${OutputfMRI} $FrameMergeSTRING $TR_vol
${FSLDIR}/bin/fslmerge -tr ${OutputfMRI}_mask $FrameMergeSTRINGII $TR_vol

[glasserm]

I assume we would use bc instead of adding a perl dependency, but this does seem worth fixing.

[cmpetty]

I assume we would use bc instead of adding a perl dependency, but this does seem worth fixing.

Good point .. i changed mine to

118 if [ ${TR_units} = "s" ] ; then
119         # this is fine
120         continue
121 elif [ ${TR_units} = "ms" ] ; then
122         TR_vol=$( echo "scale=4;${TR_vol} / 1000.0" | bc -l );
123 elif [ ${TR_units} = "us" ] ; then
124         TR_vol=$( echo "scale=4;${TR_vol} / 1000000.0" | bc -l );
125 fi

[mharms]

@cmpetty Would you be willing to create a PR for this, including finding other instances in the code base where we set the TR as part of fslmerge? Thanks.

[cmpetty]

@cmpetty Would you be willing to create a PR for this, including finding other instances in the code base where we set the TR as part of fslmerge? Thanks.

Sure. i found a couple other places ( hcp_fix_* , mcflirt_acc.sh , OneStepResampling.sh )