Dear experts,
In my final work I have to compare two methods, the manual segmentation of hippocampus and the automatic segmentation of hippocampus with FSL.
With FSL I've just used the following command:
run_first_all -i input_image -s L_Hipp,R_Hipp -o output_image
and I haven't used FLIRT previously. Is it necessary?
I also read about "General Advice and Workflow" in the section FIRST and after running run_first_all I've used this command to check the registration:
${FSLDIR}/bin/slicesdir -p ${FSLDIR}/data/standard/MNI125_T1_1mm.nii.gz *_to_std_sub.nii.gz
I actually can see brain images in different views but I can't see the red lines. Is this related with FLIRT?
Best regards,
Ana Arruda
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