Greetings FSL experts,
A few months ago, I had to uninstall and reinstall FSL 6.0 on my personal MacBook Pro. FSL was removed completely via the terminal. After reinstalling, I ran some basic preprocessing steps (see below) on diffusion data, however the brain extraction no longer worked (tested 45 subjects, all had the same issue). I tried looking over the email archive, but couldn't find any relevant postings about this issue with version 6.0. I sort of gave up and continued working on things from the desktop in my lab. Recently though, I decided to try again on the same data from before. All of a sudden, bet worked perfectly fine! This is very confusing to me and now I don't know whether or not I can trust that the software installation on my machine is working consistently. In addition to this, a colleague of mine is having the exact same problem after uninstalling and reinstalling on a Mac desktop. Any thoughts? Am I missing something? Thanks in advance for your help!
eddy_correct $1 $1_gdc_ec 0
fdt_rotate_bvecs $1.bvec $1_rot.bvec *.ecclog
bet $1_gdc_ec brain -m -n -f 0.3
dtifit -k $1_gdc_ec -o $1_gdc_ec -m brain_mask -r $1_rot.bvec -b $1.bval -w
fsleyes $1_gdc_ec_FA.nii.gz
Best,
Stephanie Otto
Graduate Student, Cognitive and Brain Sciences Program
Department of Psychology, MSS 414/MS0296
University of Nevada, Reno
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