Hey Markus,
Thanks a lot for your input. That is an excellent point. Could "too many input arguments" actually refer to "too many intermediate brain mask files" in our 4D data.nii.gz? Should one brain mask correspond to only one data slice? Which seems to be the case for intermediate files of FSL example data: "data_slice_0000.nii.gz" and "nodif_brain_mask_slice_0000.nii.gz". Yet there are 65 data slices and 160 brain maskes with our data.
Under our data.bedpostX directory, there are 8 files/folders as shown in the attachment:
5 files:
monitor
commands.txt
nodif_brain_mask.nii.gz
bvecs
bvals
3 folders:
logs
xfms
diff_slices (the bedpostX directory of FSL sample data doesn't have this folder)
Again, thank you very much for your help.
Rick
----- Original Message -----
From: Markus Gschwind <[log in to unmask]>
Date: Monday, October 6, 2008 5:40 am
Subject: Re: [FSL] BEDPOSTX Error (FDT Diffusion)
To: [log in to unmask]
> Hi Rick!
>
> It seems as besdpostX started correctly, but then found some double
> names/files in your data ("too many input arguments"). The
> intermediatefiles that were created are in this context, as
> normally they are cleared at
> the end.
>
> With your setup (WMVare) I'd expect ~24 hours of bedposting. Thus, the
> problem occurs quite at the beginning (25 min).
>
> What gives bedpostx_datacheck on your bedpost directory?
>
> The second error message (FslData) is normal, dont worry.
>
> Hope this helps,
> Markus
>
>
>
>
> 2008/10/5 Xin Li <[log in to unmask]>
>
> > Dear FSL Users,
> >
> > When I ran BEDPOSTX with FSL feeds sample data (fdt_subj1) and
> our data, it
> > prompted
> > similar error messages as shown in the attachment. BEDPOSTX
> didn't create
> > any "merged_[]'' or "mean_[]" files using our data while it still
> succeeded> with the sample data despite the error message.
> >
> > Another interesting thing is that BEDPOSTX did work on our data
> for ~25
> > minutes before giving the error and created some intermediate
> files in the
> > same folder as the input files:
> >
> > data_slice_0000.nii.gz
> > ...
> > data_slice_0065.nii.gz
> > nodif_brain_mask_slice_0000.nii.gz
> > ...
> > nodif_brain_mask_slice_0159.nii.gz
> >
> > My system is as below:
> >
> > FSL 4.1.0
> > CentOS 5 32 bit and VMware Player (FSL-vm5_32).
> > Windows XP Professional Ver 2002 SP2
> > Pentium D CPU 3.46GHz, 2.00GB of RAM
> >
> > BEDPOSTX parameters:
> > Fibres: 2
> > Weight: 1
> > Burn In: 1000
> >
> > Our data header is also attached.
> >
> >
> > Could anyone please tell me what could cause this and how to
> resolve it?
> >
> > Thank you very much,
> >
> > Rick
> >
>
>
>
> --
> Dr. med. Markus Gschwind, M.D.
> Laboratory for Neurology and Imaging of Cognition
> Dept of Neurosciences
> University Medical Center (CMU)
> 1 Michel-Servet - 1211 GENEVA - CH
>
> Tel 0041 (0) 22 379 5324
> Fax 0041 (0) 22 379 5402
> email: [log in to unmask]
> http://labnic.unige.ch
>
> PS: Switzerland is a good place for scientists. It is the origin of
> specialrelativity (1905) and the World Wide Web (1990), it is
> associated with 105
> Nobel laureates, and boasts the world's highest number of Nobel
> prizes per
> capita, the highest number of publications per capita, the highest
> number of
> patents per capita, the highest citation impact factor, the most cited
> single-author paper, etc. Switzerland also got the highest ranking
> in the
> list of happiest countries :-) .
>
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