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Dear Paul,

BET print "finished", my computer have enough memory and hard drive 
space, i.e., 64GB and 1.25T.

I have also tried BET with FSL 5.0.10 in my computer. The output file 
still collapse.

Thanks very much for your help.

Best regards,

Liangqiong

在 11/29/18 5:58 AM, paul mccarthy 写道:
> Does BET print any error? Could it be that you are low on hard drive space?
>
> Could you try running BET with FSL 5.0.11?
>
> Cheers,
>
> Paul
>
> On Wed, 28 Nov 2018 at 20:31, QU Liangqiong
> <[log in to unmask]> wrote:
>> I have ensured that the input file of my fsl and my colleague's is
>> identical the same. md5sum verifies it.
>>
>> 在 11/28/18 11:57 AM, Tim Sch äfer 写道:
>>> The gzip error suggests that the file is broken. You may want to ensure that the file is identical to the one your colleague is using (e.g., use the `md5` command on both files and compare the output).
>>>
>>>
>>>> On November 28, 2018 at 3:34 PM QU Liangqiong <[log in to unmask]> wrote:
>>>>
>>>>
>>>> Dear Pual,
>>>>
>>>> I used the following command for skull stripping （ MPRAGE_PVS46 is the
>>>> input and MPRAGE_PVS46_brain is the output）.
>>>>
>>>> /usr/local/fsl/bin/bet  MPRAGE_PVS46 MPRAGE_PVS46_brain  -f 0.2 -g 0
>>>>
>>>> When I tried to extract the .nii.gz file, the following error shows:
>>>>
>>>> gzip: MPRAGE_PVS46_brain.nii.gz: unexpected end of file
>>>>
>>>>
>>>> BTW, it is quite peculiar that the size of output file
>>>> MPRAGE_PVS46_brain.nii.gz is only 8.7kb.
>>>>
>>>> Actually all the commands of fsl also collapse, for example, the
>>>> following registration operation:
>>>>
>>>> /usr/local/fsl/bin/flirt -in MPRAGE_PVS46.nii.gz -ref
>>>> /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out
>>>> MPRAGE_PVS46_o.nii.gz -omat MPRAGE_PVS46_o.mat -bins 256 -cost corratio
>>>> -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12  -interp
>>>> trilinear
>>>>
>>>>
>>>> Best regards,
>>>>
>>>> Liangqiong
>>>>
>>>>
>>>> On 2018/11/28 上午6:03, paul mccarthy wrote:
>>>>> Hi Liangqiong,
>>>>>
>>>>> Can you please share the command that you used, and the error that you
>>>>> got when you tried to extract the .nii.gz file?
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Paul
>>>>>
>>>>> On 27/11/2018, QU Liangqiong <[log in to unmask]> wrote:
>>>>>> Dear FSL experts,
>>>>>>
>>>>>>
>>>>>> Recently, I have installed FSL6.0 on my computer (Ubuntu16.04). All the
>>>>>> installation went well, and I can open fsl in the terminal.  The echo
>>>>>> $FSLDIR returns  /usr/local/fsl. The   flirt -version displays  FLIRT
>>>>>> version 6.0.
>>>>>>
>>>>>> But when I used fsl do some mr image pre-processing, i.e., skull-strip or
>>>>>> image registration. The output file seems weird.
>>>>>>
>>>>>> For example: an original 10M T1 images after skull-strip resulted in an
>>>>>> output file with size only 8.7kb.  When I open the output file, it is all
>>>>>> dark, nothing in it.  BTW, an error occured while I extract the *nii.gz
>>>>>> output files.
>>>>>>
>>>>>> This is not due to the wrong parameter settings, since the same image files
>>>>>> and parameters settings on my colleagues's computer work well.
>>>>>>
>>>>>> Except the skull-strip, all the others' image processing in FSL also results
>>>>>> in empty output.
>>>>>>
>>>>>>
>>>>>> I have uinstall the fsl, and installed it again. But the same situation
>>>>>> still occurs in my computer.
>>>>>>
>>>>>>
>>>>>> Could you give me some advice on this?
>>>>>>
>>>>>> I am looking forward for your feedback.
>>>>>>
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Liangqiong
>>>>>>
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