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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