Hey Markus,
Our DTI protocol gives a structural data besides the diffusion data. Brain mask was initially created from the structural one. Now I use BET on the diffusion file. BEDPOSTX is still working on it and seems to be fine so far.
Thanks a lot for your help.
Rick
----- Original Message -----
From: Markus Gschwind <[log in to unmask]>
Date: Monday, October 6, 2008 3:41 pm
Subject: Re: [FSL] BEDPOSTX Error (FDT Diffusion)
To: [log in to unmask]
> Sorry, it is me again.
>
> I just saw that your bvals have 65 words and not 66. Thus
> I would expect the dimension of your mask as follows:
> dim1 128
> dim2 128
> dim3 66
> dim4 1
>
> and not as I wrote in my previous post.
> Cheers, Markus
>
>
> 2008/10/6 Markus Gschwind <[log in to unmask]>
>
> > Hi Rick!
> >
> > So, that's what was to be expected.
> >
> > /mnt/hgfs/VMW_Shared/bedpostx/data
> > data_type INT16
> > dim1 128
> > dim2 128
> > dim3 66
> > dim4 65
> >
> > This looks good!
> >
> > /mnt/hgfs/VMW_Shared/bedpostx/nodif_brain_mask
> > data_type INT16
> > dim1 512
> > dim2 512
> > dim3 160
> >
> > This, however, looks a little strange.
> > How did you create this mask? It has completely different
> dimensions.> The dimensions of the brainmask that you would
> normally get from BET (by
> > clicking the option "create binary brain mask") and which you
> would rename
> > to "nodif_brain_mask", would be:
> > dim1 128
> > dim2 128
> > dim3 1
> > dim4 65
> >
> > Try to create the correct mask, and retry bedpostx_datacheck!
> >
> > Good luck!
> >
> > Markus
> >
> >
> >
> >
> > 2008/10/6 Xin Li <[log in to unmask]>
> > >
> > > 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 :-) .
> > > >
> >
> >
> >
> > --
> > 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 special
> > relativity (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 :-) .
>
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