Hi Marvin,
You should be able to fix this problem by running the following
command (you may need to prefix it with sudo):
$FSLDIR/fslpython/bin/conda install -n fslpython -c conda-forge deprecation==1.*
Cheers,
Paul
On Fri, 5 Jul 2019 at 08:57, Saad Jbabdi <[log in to unmask]> wrote:
>
> It looks like it. Although fsl_anat is a shell script, it does call python scripts internally. I *think* that you need to have python 3 installed. Please check the FSL install instructions for more info on python-FSL (or maybe Matt Webster can chime in).
>
> Cheers
> Saad
>
>
>> On 4 Jul 2019, at 17:53, Jüchtern, Marvin <[log in to unmask]> wrote:
>>
>> Dear Saad,
>>
>> thanks a lot - I didn't know this before, I tried and then this message came after a few seconds:
>> pkg_resources.ContextualVersionConflict: (deprecation 2.0 (/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages), Requirement.parse('deprecation<=2.*,>=1.*'), {'fslpy'})
>>
>> Is there a problem with my python-version maybe?
>>
>> Best regards
>>
>> Marvin
>> ________________________________
>> Von: FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag von Saad Jbabdi <[log in to unmask]>
>> Gesendet: Mittwoch, 3. Juli 2019 01:39:56
>> An: [log in to unmask]
>> Betreff: Re: [FSL] Issue with bet
>>
>> Hi Marvin
>>
>> Have you tried fsl_anat? It uses MNI registration for more robust brain extraction.
>>
>> Cheers
>> Saad
>>
>> > On 3 Jul 2019, at 06:40, Marvin Jüchtern <[log in to unmask]> wrote:
>> >
>> > Dear all,
>> >
>> > I want to bet the T1 images for several subjects of my DTI tractography study to use them further for registration purposes.
>> >
>> > But with one subject I really struggle to extract the brain entirely out of the skull since the cortex is very close to the bone at some points. There is always a leftover of the inner skull at some parietal and frontal parts of the brain.
>> > I tried everything I found on the internet: cropping the brain via robustfov, adding -R, adding different -f and -g (also individually) and defining an image centre with -c.
>> > These parameters help a little bit, at some points the skull is gone (together with some rests at the lower parts of the brain but that's alright) but still there are huge leftovers at several points.
>> >
>> > Do you have any other (more advanced?) suggestions how to eliminate these combs/crests of skull on my brain? Maybe something manual?
>> >
>> > Thank you so much in advance!
>> >
>> >
>> > Kind regards from Germany,
>> >
>> > Marvin, Clinical Cognition Sciences, UK Aachen
>> >
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