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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