Hey Markus,
Thanks for the detailed instruction. Seems that is indeed the problem. bedpostx_datacheck reports "data dimensions do not match mask dimensions", which confirms the speculation.
Thanks again,
Rick
----- Original Message -----
From: Markus Gschwind <[log in to unmask]>
Date: Monday, October 6, 2008 1:48 pm
Subject: Re: [FSL] BEDPOSTX Error (FDT Diffusion)
To: Xin Li <[log in to unmask]>
> Hi Rick!
>
> The diff_slices directory gets cleared at the end. Thus, its
> existence tells
> us that the process is not terminated.
>
> Please do the following:
> 1) change the name of your data directory into bedpostx (the
> bedpost process
> will create the bedpostx.bedpostX directory from this.
>
> 2) then going into bedopostx, you type
> "bedpostx_datacheck ." (without the "")
>
> 3) then post this output here, please!
>
> Cheers,
> Markus
>
>
>
> 2008/10/6 Xin Li <[log in to unmask]>
>
> > 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 :-) .
> > >
> >
> >
>
>
> --
> 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 :-) .
>
