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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--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Forschung - Klinische Bildgebung
Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters
Universitätsklinikum Frankfurt / Haus 93, Raum A 305
Deutschordenstr. 50, 60528 Frankfurt am Main
Email: [log in to unmask] Tel.: +49 (0)69 6301 85832
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