[Neurodebian-users] FSL Topup failure

Morgan Hough morgan.hough at gmail.com
Tue Feb 4 22:02:05 GMT 2020


Hey Nan,

Sorry for the delay. My guess is that you have different FSL binaries
installed in your /usr/bin since NeuroDebian will install them in

/usr/share/fsl/5.0/

which you should set as your FSLDIR

# FSL Setup
FSLDIR=/usr/share/fsl/5.0
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH
. ${FSLDIR}/etc/fslconf/fsl.sh

You will need to remove the binaries in /usr/bin though. I just don't know
what you have in there. Since you didn't have the FSLDIR set maybe check if
they are symlinks for tools you wanted? Once they are removed, set your
FSLDIR and you will be using the binaries from /usr/share/fsl/5.0. That way
you can install FSL 6.0 too of course and just change FSLDIR when you want
to switch.

Hopefully that will now work for you.

Cheers,

-Morgan

On Mon, Feb 3, 2020 at 4:06 AM Nan Xu <nxu at u.rochester.edu> wrote:

> 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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