Hi Stephanie,
How does the image which for which BET did not work compare with the
original non-brain-extracted input image?
Paul
On 29/07/2019, Stephanie Otto <[log in to unmask]> wrote:
> Hi Paul,
>
> My apologies for any ambiguity. When I say the brain extraction no longer
> worked, I mean that the head and neck were not removed. I assume this is
> because bet did not work properly. I tried to attach a screenshot of the
> same subject that was preprocessed on the same machine with the same FSL
> download (after reinstalling the software), but at different time points.
> That email was rejected though because of the size of the attachments. The
> threshold that was used for bet was the same for each run (0.3). I haven't
> run any further analysis on my laptop because I'm not sure if something
> went wrong with the software download, which makes me question if it is
> reliable. I haven't received any error messages during the preprocessing
> either. Thanks for all your help!
>
> Best,
> Stephanie Otto
> Graduate Student, Cognitive and Brain Sciences Program
> Department of Psychology, MSS 414/MS0296
> University of Nevada, Reno
> [log in to unmask]
>
>
>
> On Sun, Jul 28, 2019 at 2:42 AM paul mccarthy <[log in to unmask]>
> wrote:
>
>> 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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>> >
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