Dear Dr. Jenkinson:
Thank you for your advice.
However, I found it still not worked if I followed your suggestion.
The attached is the log file of fmNc01.nii.gz after FIRST.
The following problems still appeared
I found I couln't view the mesh (.vtk) file in the fslview as I saw before in the previous set of data.
> > > > >
> > > > > Besides, there was no any subcortical structural data could be shown in the FSLVIEW after FIRST segmentation (mesh file, the volume file after conversion from mesh file) and
> > > > >
> > > > > The similar wrong message also showed " 16935 Segmentation fault ${FSLDIR}/bin/fslview.app/Contents/MacOS/fslview $@".
Can you teach how to debug in the following?
Thank you.
Dr. Lai
--- 11/5/25 (三)，Mark Jenkinson <[log in to unmask]> 寫道：
寄件者: Mark Jenkinson <[log in to unmask]>
主旨: Re: [FSL] FW： Re: [FSL] questions about FIRST segmentation faults
收件者: [log in to unmask]
日期: 2011年5月25日,三,下午3:39
Dear Dr Lai,
I could not view the original file due to an unusual datatype
that is not yet supported by FSLView (although other tools
should have been OK). However, to start with I ran the following:
fslmaths NC01 fmNC01
which made a new file (fmNC01) that I could view with FSLView.
The image looked fine (and has *lots* of FOV down into the neck
so it is definitely not a brainstem/FOV issue).
I then used run_first_all and it completed fine on my machine
(running it on fmNC01) and gave me a good result.
So try running the above fslmaths command and then see if you
can get run_first_all to work on the resulting image.
All the best,
Mark
On 25 May 2011, at 03:17, Chien-Han Lai wrote:
> Dear Dr. Jenkinson:
>
> Sorry for the missing errors.
>
> The reference number 469618, which include the zip file and original file (NC01.nii)
>
> Thank you.
>
> Dr. Lai
>
> --- 11/5/24 (二)，Mark Jenkinson <[log in to unmask]> 寫道：
>
> 寄件者: Mark Jenkinson <[log in to unmask]>
> 主旨: Re: [FSL] FW： Re: [FSL] questions about FIRST segmentation faults
> 收件者: [log in to unmask]
> 日期: 2011年5月24日,二,下午5:02
>
> Dear Dr Lai,
>
> I'm afraid there were no files uploaded and we have checked
> that the upload site is working correctly. Can you please try
> and upload the files again.
>
> All the best,
> Mark
>
>
> On 24 May 2011, at 03:12, Chien-Han Lai wrote:
>
> > Dear Dr. Jenkinson:
> >
> > The upload reference number is 935299.
> >
> > Hope we can find the answer.
> >
> > Thank you for your kind help.
> >
> > Dr. Lai
> >
> >
> > --- 11/5/23 (一)，Mark Jenkinson <[log in to unmask]> 寫道：
> >
> > 寄件者: Mark Jenkinson <[log in to unmask]>
> > 主旨: Re: [FSL] FW： Re: [FSL] questions about FIRST segmentation faults
> > 收件者: [log in to unmask]
> > 日期: 2011年5月23日,一,下午4:43
> >
> > Dear Dr Lai,
> >
> > All of the *.e* files you sent me were empty (of zero length).
> > This is not an indication of an error - this means that there
> > was no error. So it does not look like this is the problem.
> > When you look at these in future, use the cat *.e* command
> > as used in the documentation, as that only shows you the
> > non-zero contents which indicate an error.
> >
> > As for diagnosing your original problem I think the only way
> > to know is if you send us the directory with all the relevant
> > files (just for one subject where you have the problem).
> > You can do this via our upload site at:
> > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> > and don't forget to also send us the reference number of the
> > upload.
> >
> > All the best,
> > Mark
> >
> >
> > On 23 May 2011, at 02:27, Chien-Han Lai wrote:
> >
> > > Dear Dr. Jenkinson:
> > >
> > > I ever checked the slicerdir directory of the registraion output data.
> > >
> > > It seemed that the registration was fine.
> > >
> > > The attached is the compressed file of the log file.
> > >
> > > Please take look at these files and see if there any suggestions to debug this problem.
> > >
> > > Sorry to cause your inconvenience and thank you for your kind help.
> > >
> > > Dr. Lai
> > >
> > > --- 11/5/22 (日)，Mark Jenkinson <[log in to unmask]> 寫道：
> > >
> > > 寄件者: Mark Jenkinson <[log in to unmask]>
> > > 主旨: Re: [FSL] FW： Re: [FSL] questions about FIRST segmentation faults
> > > 收件者: [log in to unmask]
> > > 日期: 2011年5月22日,日,上午4:47
> > >
> > > Dear Dr Lai,
> > >
> > > I need to see the content of these slides, although it looks
> > > like the registration has failed if there is a first_flirt error file.
> > > Have you checked the registration outputs, as recommended
> > > in the web page documentation?
> > >
> > > All the best,
> > > Mark
> > >
> > >
> > > On 21 May 2011, at 02:58, Chien-Han Lai wrote:
> > >
> > > > The e files are as follows
> > > >
> > > > clean_up.e15313.1
> > > > first_flirt.e8698
> > > > first_post.e15298.1
> > > > first.e8915
> > > >
> > > > Thank you.
> > > >
> > > > Dr. Lai
> > > >
> > > > --- 11/5/21 (六)，[log in to unmask] <[log in to unmask]> 寫道：
> > > >
> > > > 寄件者: [log in to unmask] <[log in to unmask]>
> > > > 主旨: Re: [FSL] questions about FIRST segmentation faults
> > > > 收件者: "FSL - FMRIB's Software Library" <[log in to unmask]>
> > > > 日期: 2011年5月21日,六,上午9:23
> > > >
> > > > Dear Dr. Jenkinson:
> > > >
> > > > Thank you for your kind reply.
> > > >
> > > > The attached is the log file and it seems with some .*e* files.
> > > >
> > > > Besides, below is our 3T MRI pulse sequence for structural imaging
> > > >
> > > > (TR 2530ms； TE 3.03ms；slice thickness= 1mm（no gap）；192slices；matrix = 224x256；field of view: 256mm；number of excitation=1)
> > > >
> > > > I don't know if the FOV too short for the cover of brainstem.
> > > >
> > > > As you suggested, how should I set the list except brainstem?
> > > >
> > > > Thank you for your kind help.
> > > >
> > > > Sincerely yours
> > > >
> > > > Dr. Lai
> > > >
> > > > --- 11/5/20 (五)，Mark Jenkinson <[log in to unmask]> 寫道：
> > > >
> > > > 寄件者: Mark Jenkinson <[log in to unmask]>
> > > > 主旨: Re: [FSL] questions about FIRST segmentation faults
> > > > 收件者: [log in to unmask]
> > > > 日期: 2011年5月20日,五,下午6:55
> > > >
> > > > Dear Dr Lai,
> > > >
> > > > Can you look at the log files and tell us if there were any errors
> > > > reported (the *.e* files - see the FIRST documentation page at
> > > > http://www.fmrib.ox.ac.uk/fsl/first/index.html
> > > > under General Advice and Workflow).
> > > >
> > > > We need to know more details in order to be able to help.
> > > > One problem which might cause this is if the FOV of the image
> > > > is a bit short in the inferior direction so that it does not cover
> > > > all the brainstem. If this is the case then try using run_first_all
> > > > with a list of structures that excludes the brainstem.
> > > >
> > > > All the best,
> > > > Mark
> > > >
> > > >
> > > > On 20 May 2011, at 11:32, Chien-Han Lai wrote:
> > > >
> > > > > Dear all FSL experts:
> > > > >
> > > > > I probably have a technique issue for the FIRST segmentation faults.
> > > > >
> > > > > I ever run the FIRST well on my previous MDI data and the mesh file is fine without segmentation faults.
> > > > >
> > > > > However, I tried FIRST on another set of MRI data, I found I couln't view the mesh (.vtk) file in the fslview as I saw before in the previous set of data.
> > > > >
> > > > > Besides, there was no any subcortical structural data could be shown in the FSLVIEW after FIRST segmentation (mesh file, the volume file after conversion from mesh file) and
> > > > >
> > > > > The wrong message was as follows " 16935 Segmentation fault ${FSLDIR}/bin/fslview.app/Contents/MacOS/fslview $@".
> > > > >
> > > > > I don't understand why the FIRST can't work in another set of data.
> > > > >
> > > > > Can anybody help me and give me some suggestions?
> > > > >
> > > > > Thank you.
> > > > >
> > > > > Dr. Lai
> > > <NC01.logs.rar>
