[Neurodebian-users] FSL Topup failure

[Nan Xu]

Hi Morgan,

topup is located in the same directory as fslino (/usr/bin), but if I open
the topup file, I see a 1 line command (../lib/fsl/5.0/fsl_app_wrapper).
the topup command does return a log file (see attached) although it reports
"Segmentation fault (core dumped)".
fslinfo runs with no problem (see below). In fact, all other fsl functions
I have tested so far run very well. I have uninstalled and reinstalled
fsl-complete. I still get the same errors.
echo $FSLDIR returns nothing.

$ which fslinfo
/usr/bin/fslinfo
$ which topup
/usr/bin/topup

$ topup --imain=rrpEPI_fsl_swap.nii.gz --datain=datain_topup.txt
--config=EPI_topup_HLL_fix.cnf --out=test
Segmentation fault (core dumped)

$ fslinfo EPI_fsl_swap.nii.gz
data_type      FLOAT32
dim1           64
dim2           32
dim3           16
dim4           2
datatype       16
pixdim1        3.000000
pixdim2        3.000000
pixdim3        6.000000
pixdim4        2.000000
cal_max        201.1975
cal_min        0.0025
file_type      NIFTI-1+

$echo $FSLDIR


On Mon, Feb 3, 2020 at 1:36 AM Morgan Hough <morgan.hough at gmail.com> wrote:

> 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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