Hi,
If the image files (nii.gz) are all fine then everything should be OK.
Just convert the vtk files to ascii if you want to individually view them,
although this isn't necessary if all you want to do is run vertex analysis.
The output from vertex analysis will be ascii and viewable without
conversion.
All the best,
Mark
On 28 May 2011, at 05:27, Chien-Han Lai wrote:
> Dear Dr. Jenkinson:
>
> Thank you for your kind reply.
>
> The FSL I run is version 4.1.6, which should be not too old version.
>
> Besides, the image files (the nii.gz files) are fine under FSLVIEW. I will try to see if that binary command will fix the vtk problems, because the following analysis and meshToVol command will all use the vtk files, so if the vtk file is with problem, then the following steps will be with mistakes.
>
> Thank you.
>
> Best
>
> Dr. Lai
>
> --- 11/5/27 (五)，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27日,五,下午3:51
>
> Dear Dr Lai,
>
> There are still no errors in these log files.
> Are you sure that you do not have an image file output?
> What version of FSL are you running?
>
> If you are only having trouble viewing the mesh (but
> the image is OK) then it is probably because of the
> binary format in the vtk file which can be fixed with:
> run_mesh_utils --doConvert_Binary_To_ASCII -m original_file.vtk -o new_file.vtk
>
> I am just unsure what is currently being created or not
> and what you can and cannot view. As there are no
> errors and it all worked well at my end on your data I
> am assuming that it is just a vtk issue that you can fix
> it with the above command.
>
> If you are not getting the image output, or not getting the
> vtk file generated in the first place, then please let me
> know and include the result of "ls -lrt" on your output directory
> so that I can see what is and what is not created.
>
> All the best,
> Mark
>
>
>
> On 27 May 2011, at 02:34, Chien-Han Lai wrote:
>
> >
> > 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>
> > <fmNC01.logs.rar>
