Hi Liangqiong,
Do the FSL tools work if you set the FSLOUTPUTTYPE environment
variable to NIFTI?
e.g.
export FSLOUTPUTTYPE=NIFTI
bet ....
Cheers,
Paul
On 29/11/2018, QU Liangqiong <[log in to unmask]> wrote:
> 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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