That might be worth it since when testing the script I still get:
[fslchfiletype NIFTI_GZ OAS1_0001_MR1_mpr-1_anon.hdr /data/3DCNN/data/
/home/robka/fsl/bin/fslchfiletype: line 90: 6744 Segmentation fault (core dumped) $FSLDIR/bin/fslchfiletype_exe $1 $oldfile $newfile
Strange that it worked for the other user who probably back then used an even older FSL version?
Updated fsl
flirt -version still says 6.0 but the GUI says 6.0.3
Now it works! Thanks to both of you =)
Now I plan to run
#preform fslstd
fslreorient2std $p $output_main/$out_folder/T1_${sub_number}_std.nii
#preform robustfov
robustfov -i $output_main/$out_folder/T1_${sub_number}_std.nii.gz -r $output_main/$out_folder/T1_${sub_number}_std_fov.nii
#preform BET
$FSLDIR/bin/bet $output_main/$out_folder/T1_${sub_number}_std_fov.nii.gz $output_main/$out_folder/T1_${sub_number}_brain.nii -f 0.4
I do notice that the skull-strip still is not perfect, there are some extra tissue at the bottom of the brain. Apart from adding -S to bet (if the eyes are there) is there anything else I can do?
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