Dear Paul,
Cool. That works. It seems that it is the gz problem.
Thanks very much for your help.
Best regards,
Liangqiong
On 2018/12/3 上午9:09, paul mccarthy wrote:
> 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
>>>>>>>>
>>>>>>>> ########################################################################
>>>>>>>>
>>>>>>>> To unsubscribe from the FSL list, click the following link:
>>>>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>>>>>>
>>>>>>> ########################################################################
>>>>>>>
>>>>>>> To unsubscribe from the FSL list, click the following link:
>>>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>>>> ########################################################################
>>>>>>
>>>>>> To unsubscribe from the FSL list, click the following link:
>>>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>>> ########################################################################
>>>>
>>>> To unsubscribe from the FSL list, click the following link:
>>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>> ########################################################################
>>>
>>> To unsubscribe from the FSL list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>> .
>>>
>> ########################################################################
>>
>> To unsubscribe from the FSL list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|