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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