Keren,
If you look inside your log file, it should give you more complete information about the problem. I would guess it's still trying to transform some image for you, so it's trying to apply that empty matrix.
When we use ANTs registrations, we run something like the following after our first-level FEATs to prepare for the higher-level.
mkdir -p ${FeatDir}/reg/
cp Project/Standard/StandardANTsTemplate.nii.gz ${FeatDir}/reg/standard.nii.gz
touch ${FeatDir}/reg/example_func2standard.mat
mkdir -p ${FeatDir}/stats/
WarpImageMultiTransform 3 ${FeatDir}/example_func.nii.gz ${FeatDir}/reg_standard/example_func.nii.gz -R ListOfTransforms
WarpImageMultiTransform 3 ${FeatDir}/mean_func.nii.gz ${FeatDir}/reg_standard/mean_func.nii.gz -R ListOfTransforms
WarpImageMultiTransform 3 ${FeatDir}/mask.nii.gz ${FeatDir}/reg_standard/mask.nii.gz -R ListOfTransforms
for cope in ${FeatDir}/stats/cope*.nii.gz; do WarpImageMultiTransform 3 ${cope} ${FeatDir}/reg_standard/`basename ${cope}` -R ListOfTransforms; done
for varcope in ${FeatDir}/stats/varcope*.nii.gz; do WarpImageMultiTransform 3 ${varcope} ${FeatDir}/reg_standard/`basename ${varcope}` -R ListOfTransforms; done
________________________________________
From: Keren Lesinger <[log in to unmask]>
Sent: Wednesday, July 8, 2015 8:31 AM
To: [log in to unmask]; Katie Askren
Cc: Keren Lesinger
Subject: Re: FEAT second level analysis with standard space from ants
Hi
Thanks for your reply.
I created this empty mat file.
When running the Higher level analyis with feat directories option
this is the error I get:
/usr/share/fsl/5.0/bin/fsl_sub -T 60 -l logs -N feat2_pre /usr/share/fsl/5.0/bin/feat /media/gidonro/DATA/keren/finalProcessing/Thesis/AR_BL.gfeat/design.fsf -D /media/gidonro/DATA/keren/finalProcessing/Thesis/AR_BL.gfeat -gfeatprep
while executing
"fsl:exec "${FSLDIR}/bin/feat ${fsfroot}.fsf -D $FD -gfeatprep" -b 60 -N feat2_pre -l logs "
invoked from within
"if { $done_something == 0 } {
if { ! $fmri(inmelodic) } {
if { $fmri(level) == 1 } {
for { set session 1 } { $session <= $fmri(multiple..."
(file "/usr/share/fsl/5.0/bin/feat" line 389)
when I try to run it using copes images transformed to standard I still get the error that asks me to do registration.
i will appreciate your advice/
Thanks
Keren
|