Thanks Danny, that explains the error (we used fieldmap-corrected BBR, nonlinear warping for EPI to T1, so we generate example_func2standard_warp instead of example_func2standard.mat).
but it begs the larger question of why we can't use our fieldmap-corrected, BBR nonlinear epi to T1 warp with featregapply?
for example, with featregapply:
if { [ imtest reg/highres2standard_warp ] && ( $space == "example_func" || $space == "highres" ) } {
set PREMAT ""
if { $space == "example_func" } {
set PREMAT "--premat=reg/example_func2highres.mat"
}
if { $interp == "nearestneighbour" } {
set interp nn
}
fsl:exec "${FSLDIR}/bin/applywarp --ref=$ref --in=$in --out=$TMPNAM --warp=reg/highres2standard_warp $PREMAT --interp=$interp"
Why can't we use the fieldmap-corrected BBR, nonlinear epi to T1 and do something like:
if { [ imtest reg/highres2standard_warp ] && ( $space == "example_func" || $space == "highres" ) } {
set WARP1 ""
if { $space == "example_func" } {
set WARP1 "--warp1=reg/example_func2highres_warp"
}
if { $interp == "nearestneighbour" } {
set interp nn
}
##Sum nonlinear transforms (rough syntax)
fsl:exec "${FSLDIR}/bin/convertwarp --ref=$ref --in=$in --warp1=$WARP1 --warp2=reg/highres2standard_warp --out=reg/example_func2standard_warp --relout
#Use the combined warps (rough syntax)
fsl:exec "${FSLDIR}/bin/applywarp --ref=$ref --in=$in --out=$TMPNAM --warp=reg/example_func2standard_warp --interp=$interp"
>
>Hmm.. looking at the code for featregapply, you get that error msg if featregapply cannot locate example_func2standard.mat in the reg folder.
>--- line 162 ---
>if { ! [ file exists reg/example_func2standard.mat ] } {
> puts "Error - registration has not been run for [ pwd ]"
> exit 1
>}
>-------------------
>
>See if example_func2standard.mat exists for each feat/reg folder. If they do exist, check permission settings so that you are able to read those .mat >files.
>
>Best,
>
>Danny Kim
>
>On 2015-04-15, at 3:44 PM, Matt Sutterer wrote:
>
>> Hi Danny,
>>
>> The FEAT GUI will not allow me to run the higher-level analysis, I get a pop-up with the error about registration not being run. If I run my .fsf through the feat command line, the feat log shows errors at the "Higher-level input files preparation" stage:
>>
>> Higher-level input files preparation
>>
>> /usr/fsl/bin/featregapply /ppg/resting_state/NSG_acute/284_chronic/rsOut1/reproc/nuisancereg.feat
>> Error - registration has not been run for /ppg/resting_state/NSG_acute/284_chronic/rsOut1/reproc/nuisancereg.feat
>>
>> /usr/fsl/bin/featregapply /ppg/resting_state/NSG_acute/284_chronic/rsOut2/reproc/nuisancereg.feat
>> Error - registration has not been run for /ppg/resting_state/NSG_acute/284_chronic/rsOut2/reproc/nuisancereg.feat
>>
>> ...and so on...
>>
>> things continue to fail from there, presumably because of the initial failure of featregapply.
>>
>> highres2standard.mat is present in the session.feat/reg folder for each session.
>>
>> Thanks much,
>>
>> Matt Sutterer
>>
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