Hi
Have looked in the archives but cant seem to find the answer
I am running matlab locally on my mac
I have also installed fsl and command line tools
The startup.m file has the necessary fsl code as below:
setenv('FSLDIR','/usr/local/fsl');
setenv('FSLOUTPUTTYPE','NIFTI_GZ');
fsldir = getenv('FSLDIR');
fsldirmpath = sprintf('%s/etc/matlab',fsldir);
path(path, fsldirmpath);
clear fsldir fsldirmpath;
I am trying to run a matlab script to analyse some fmri data
Once I am in the correct directory, to use fsl tools like fslmaths and flirt, am I correct that I still have to enter:
system('$FSLDIR/bin/bet struc.nii.gz struc_brain -B');
in the matlab script?
I would also like to call some other scripts such as asl_calib that are in the FSL install
Do I need to go through the whole of asl_calib locally and change the path of all commands such as fslmaths to $FSLDIR/bin/fslmaths as my matlab script seems not to recognise these fsl commands
Or is there an easier way?
thanking you in advance
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