[Neurodebian-users] FSL Topup failure

[Morgan Hough]

Hey Nan,

Hmm. And “which topup” gives you the same path? I forget if topup is a
script or a binary. You can less `which topup` and see.

Never hurts to check the input files with other binaries. Fslinfo the 4D
nifti. cat the text file. If you are getting a core dump, that is still my
guess from what you have told me.

You can remove with the same command you installed with. Check first you
have fsl-complete installed. You want to check what is happening with your
.bashrc/.profile. Echo $FSLDIR or something like that.

Cheers,

-Morgan

On Sun, Feb 2, 2020 at 21:53 Nan Xu <nxu at u.rochester.edu> wrote:

> Hi Morgan,
>
> Here’re what I have.
> 1. topup without arguments returns the usage output without problems.
> 2. input text file and the file paths should all be good because the same
> command works fine in a different Linux system which installed the FSL
> without using neurodebian.
>
> So, I’m wondering if it’s a installation problem, how to uninstall fsl and
> reinstall fsl with neurodebian?
>
> Thanks,
> Nan
>
>
> On Feb 2, 2020, at 11:27 PM, Morgan Hough <morgan.hough at gmail.com> wrote:
>
> 
>
> Ok. So try topup without arguments. You should get the usage output. If
> that works for you, check your input text file the acquisition parameters.
> Make sure it’s UNIX text friendly. Then check the paths are OK?
>
> You can test your install with FEEDS. Hope this helps.
>
> Cheers,
>
> -Morgan
>
> On Sun, Feb 2, 2020 at 13:11 Nan Xu <nxu at u.rochester.edu> wrote:
>
>> Hi Morgan,
>>
>> Yes, "which fslinfo" returns /user/bin/fslinfo
>>
>> Thanks,
>> Nan
>>
>> On Fri, Jan 31, 2020 at 2:41 PM Morgan Hough <morgan.hough at gmail.com>
>> wrote:
>>
>>> Hi Nan,
>>>
>>> Did you add the install directory to your shell’s path? What about
>>> “which fslinfo”?
>>>
>>> Cheers,
>>>
>>> -Morgan
>>>
>>> On Fri, Jan 31, 2020 at 11:37 Nan Xu <nxu at u.rochester.edu> wrote:
>>>
>>>> Hi,
>>>>
>>>>
>>>>
>>>> I have a ubuntu 18.04 WSL system. I installed the neurodebian before
>>>> install the fsl by using the command "sudo apt-get install fsl”. However, I
>>>> received the following error message when running fsl topup:
>>>>
>>>> $ topup --imain=EPI_fsl_swap --config=EPI_topup_HLL_fix.cnf
>>>> --datain=datain_topup.txt --out=tu_g --iout=tus_g -v
>>>>
>>>> Segmentation fault (core dumped)
>>>>
>>>>
>>>>
>>>> Does anyone know how to fix this problem?
>>>>
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Nan
>>>> _______________________________________________
>>>> Neurodebian-users mailing list
>>>> Neurodebian-users at alioth-lists.debian.net
>>>>
>>>> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/neurodebian-users
>>>
>>>
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