Print

---

Additionally, although FSL4 is apparently in your path (you are  
calling FSL 4 functions),
your FSLDIR is apparently set to an old FSL3 directory -
If you change this to point to the FSL4 installation, I am sure  
bedpost_datacheck will tell you your bvecs/bvals are wrong!

Cheers

T

On 21 Aug 2007, at 22:53, Andreas Bartsch wrote:

> Hi,
> you don't seem to have the data & nodif_brain_mask files in the  
> directory (which has sort of a strange path, I'd say). Furtermore,  
> you must check that your bvals has all values in a single line.
> Cheers-
> Andreas
>
> ________________________________
>
> Von: FSL - FMRIB's Software Library im Auftrag von Roger Moore
> Gesendet: Di 21.08.2007 21:46
> An: [log in to unmask]
> Betreff: Re: [FSL] using dtifit
>
>
> Hi Saad,
>
> Thanks for the reply.
>
> Okay, when I am in the directory which contains  
> 'bedpostx_datacheck' and I give directory which contains my input  
> files, I get the following:
>
> corona10% pwd
> /vol/vipdata/packages/fsl-4.0.0/bin
> corona10% ./bedpostx_datacheck /vol/vipdata/users/rjm06/itk/linux/bin
> /vol/vipdata/users/rjm06/itk/linux/bin/data
> ./bedpostx_datacheck: line 12: /vol/vipdata/packages/fsl3.3.7/bin/ 
> fslinfo: No su
> ch file or directory
>
> /vol/vipdata/users/rjm06/itk/linux/bin/nodif_brain_mask
> ./bedpostx_datacheck: line 12: /vol/vipdata/packages/fsl3.3.7/bin/ 
> fslinfo: No su
> ch file or directory
>
>  num lines in /vol/vipdata/users/rjm06/itk/linux/bin/bvals
> 2
>  num words in /vol/vipdata/users/rjm06/itk/linux/bin/bvals
> 16
>  num lines in /vol/vipdata/users/rjm06/itk/linux/bin/bvecs
> 3
>  num words in /vol/vipdata/users/rjm06/itk/linux/bin/bvecs
> 48
> ./bedpostx_datacheck: line 28: /vol/vipdata/packages/fsl3.3.7/bin/ 
> fslval: No such file or directory
> ./bedpostx_datacheck: line 29: /vol/vipdata/packages/fsl3.3.7/bin/ 
> fslval: No such file or directory
> ./bedpostx_datacheck: line 30: /vol/vipdata/packages/fsl3.3.7/bin/ 
> fslval: No such file or directory
> ./bedpostx_datacheck: line 31: /vol/vipdata/packages/fsl3.3.7/bin/ 
> fslval: No such file or directory
> ./bedpostx_datacheck: line 33: /vol/vipdata/packages/fsl3.3.7/bin/ 
> fslval: No such file or directory
> ./bedpostx_datacheck: line 34: /vol/vipdata/packages/fsl3.3.7/bin/ 
> fslval: No such file or directory
> ./bedpostx_datacheck: line 35: /vol/vipdata/packages/fsl3.3.7/bin/ 
> fslval: No such file or directory
> data dimensions do not match mask dimensions
> ./bedpostx_datacheck: line 51: [: 16: unary operator expected
> ./bedpostx_datacheck: line 54: [: 16: unary operator expected
> corona10%
>
>
> I'm sure the above will mean more to you than it does to  
> me....would be great if you could tell me how to remedy the problem.
>
> Thank you,
>
> Roger
>
>
> Saad Jbabdi wrote:
>
> 	Hi Roger,
>
> 	What does bedpost_datacheck (or bedpostx_datacheck if you're using  
> FSL4.0) give on your dtifit directory?
>
> 	Saad
>
>
> 	On 21 Aug 2007, at 17:32, Roger Moore wrote:
>
>
> 		Hello,
>
> 		I am trying to use dtifit, but so far unsuccessfully.  My command  
> line and error message are shown below.
>
> 		corona10% /vol/vipdata/packages/fsl-4.0.0/bin/dtifit -k  
> diffusion.nii.gz -o dtiout -m nodif_brain.nii.gz -r bvecfile -b  
> bvalfile -V
> 		data file diffusion.nii.gz
> 		mask file nodif_brain.nii.gz
> 		bvecs     bvecfile
> 		bvals     bvalfile
> 		reading data
> 		reading mask
> 		ok
> 		0 128 0 128 0 64
> 		setting up vols
> 		copying input properties to output volumes
> 		zeroing output volumes
> 		ok
> 		Forming A matrix
> 		terminate called after throwing an instance of  
> 'NEWMAT::IndexException'
> 		Abort
> 		corona10%
> 		It appears to happen in the function form_Amat(r,b)....but I  
> don't know why....r (bvecsfile) and b (bvalsfile) are the right  
> dimensions (3x16 and 1x16).
>
> 		If anybody could suggest what the problem might I would be very  
> grateful.
>
> 		Thank you,
>
> 		Roger
>
>
> 	
> 	--------------------------------------------------------------------- 
> ------
> 	Saad Jbabdi,
> 	Postdoctoral Research Assistant,
> 	Oxford University FMRIB Centre
>
> 	FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> 	+44 (0) 1865 222545  (fax 222717)
> 	[log in to unmask]    http://www.fmrib.ox.ac.uk/~saad
> 	--------------------------------------------------------------------- 
> ------