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.chPS: 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 :-) .
