Hi Stephanie,
You need to provide more information for us to know what has happened
- " brain extraction no longer worked" - in what way did it not work?
Were any errors printed to the terminal?
Paul
On 26/07/2019, Stephanie Otto <[log in to unmask]> wrote:
> 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
> [log in to unmask]
>
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