I am not quite sure why it is failing, but I can see that it has not correctly combined your asl to structural transformation with the structural to standard transformation. As it has not done this, it cannot find the relevant transformation and thus does not produce the standard space results. Since you already have the transformation matrices I would suggest that you do this step yourself after oxford_asl has run using flirt on the native space results. There is nothing special about the transformation that oxford_asl to get the data into standard space, the options as included to allowing everything to be done in a single command, but clearly it hasn't all quite come together in this case, sorry.
Michael
On 12 May 2014, at 21:32, R. Duke <[log in to unmask]> wrote:
> Michael,
>
> I am having a problem generating a std_space directory with any images in it. I have no problem with the first command listed below (generating native space perfusion images), but for some reason I am unable to register to standard space using the additional options in the second command (the error I get is listed at the end of this inquiry). Can you spot any obvious issues? I am using the -t option to reference my T1 to standard space matrix and the -S option to reference the 1mm MNI atlas.
>
> oxford_asl -i 001_pasl_diffdata.nii.gz -c 001_M0_brain_merge.nii.gz --tis 1.9 -o perfusion_calib_no_std --bolus 0.7 --fixbolus --tr 3.4 --te 12 --slicedt 0.0625 -s 001_t1_struct_brain.nii.gz --regfrom 001_M0_brain.nii.gz --asl2struc 001_M0_2_t1.mat --report --norm > junk_no_std.txt
>
> oxford_asl -i 001_pasl_diffdata.nii.gz -c 001_M0_brain_merge.nii.gz --tis 1.9 -o perfusion_calib_std --bolus 0.7 --fixbolus --tr 3.4 --te 12 --slicedt 0.0625 -s 001_t1_struct_brain.nii.gz --regfrom 001_M0_brain.nii.gz --asl2struc 001_M0_2_t1.mat -t 001_t1_2_std.mat -S /usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --report --norm > junk_std.txt
>
> FABBER is all done.
> Duration: 17 seconds.
> Logfile was: /tmp/fsl_lS1RcN_ox_asl/basil/step1/logfile
> End.
> Could not open matrix file /tmp/fsl_lS1RcN_ox_asl/asl2std.mat
> terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException'
> /usr/local/fsl/bin/oxford_asl: line 172: 30471 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2std.mat -ref $std -out $outdir/std_space/$subdir/$parname
> ERROR:: Empty mask image
> Cannot open volume perfusion_calib_test/std_space///perfusion for reading!
> Could not open matrix file /tmp/fsl_lS1RcN_ox_asl/asl2std.mat
> terminate called after throwing an instance of 'NEWMAT::IncompatibleDimensionsException'
> /usr/local/fsl/bin/oxford_asl: line 172: 30527 Aborted (core dumped) flirt -in $tempdir/$subdir/$param -applyxfm -init $tempdir/asl2std.mat -ref $std -out $outdir/std_space/$subdir/$parname
> ERROR:: Empty mask image
> ERROR:: Empty mask image
> ERROR:: Empty mask image
> Cannot open volume perfusion_calib_test/std_space///perfusion for reading!
> ERROR:: Empty mask image
> ERROR:: Empty mask image
> Output is perfusion_calib_test/
> OXFORD_ASL - done.
>
> Cheers,
>
> R
>
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