Yep, removing the lines fixed the DTIFit problem. Thanks!

Kristen

-----Original Message-----
From: FSL - FMRIB's Software Library
To: [log in to unmask]
Sent: 11/28/2005 5:42 PM
Subject: Re: [FSL] DTIFit/Bedpost DTI analysis error

Hi - I think that this time it's not a windows problem - the problem is 
having empty lines between the lines of text data in the bvecs file.

Cheers.



On Mon, 28 Nov 2005, Tim Behrens wrote:

> OK - next thing to check:
> 1) Did you make your bvecs/bvals files in Windows? i.e. do you have ^M

> characters instead of carriage returns if you look at them in a Unix 
> editor?
> 
> 2) Do you have a proper Unix carriage return at the end of the last
line 
> in your bvecs/bvals files?
> 
> if so, do you get an error if you run dtifit from the command line.
i.e.
> dtifit -k data -r bvecs -b bvals -m nodif_brain_mask -o dti
> 
> cheers
> 
> T
> 
> 
> 
> On Mon, 28 Nov 2005, Kristen Lindgren wrote:
> 
> > 
> > Hi Tim.  I ran bedpost_datacheck and I didn't get any errors.  The
output is
> > below.  I've also attached the bvecs and bvals files.  Any thoughts?
> > Thanks!
> > 
> > Kristen
> > 
> > 
> > 
> > dim1           128
> > dim2           128
> > dim3           73
> > dim4           16
> > datatype       4
> > pixdim1        -1.8000152111
> > pixdim2        1.7999999523
> > pixdim3        2.0000000000
> > pixdim4        1.0000000000
> > cal_max        0.0000
> > cal_min        0.0000
> > glmax          0
> > glmin          0
> > origin1        0
> > origin2        0
> > origin3        0
> > file_type      ANALYZE-7.5
> > 
> > 704301DTI//nodif
> > dim1           128
> > dim2           128
> > dim3           73
> > dim4           1
> > datatype       4
> > pixdim1        -1.8000152111
> > pixdim2        1.7999999523
> > pixdim3        2.0000000000
> > pixdim4        1.0000000000
> > cal_max        0.0000
> > cal_min        0.0000
> > glmax          0
> > glmin          0
> > origin1        0
> > origin2        0
> > origin3        0
> > file_type      ANALYZE-7.5
> > 
> > 704301DTI//nodif_brain_mask
> > dim1           128
> > dim2           128
> > dim3           73
> > dim4           1
> > datatype       4
> > pixdim1        1.8000152111
> > pixdim2        1.7999999523
> > pixdim3        2.0000000000
> > pixdim4        1.0000000000
> > cal_max        392.0000
> > cal_min        0.0000
> > glmax          0
> > glmin          0
> > origin1        0
> > origin2        0
> > origin3        0
> > file_type      ANALYZE-7.5
> > 
> >  num lines in 704301DTI//bvals 
> >        1
> >  num words in 704301DTI//bvals 
> >       16
> >  num lines in 704301DTI//bvecs 
> >        3
> >  num words in 704301DTI//bvecs 
> >       48
> > 
> > -----Original Message-----
> > From: FSL - FMRIB's Software Library
> > To: [log in to unmask]
> > Sent: 11/28/2005 5:27 PM
> > Subject: Re: [FSL] DTIFit/Bedpost DTI analysis error
> > 
> > Hi - 
> > I guess this is a problem with your bvecs/bvals files. Can you run 
> > bedpost_datacheck on your input directory as a first step to check
for 
> > errors.
> > 
> > bedpost_datacheck <indir>
> > 
> > Thanks 
> > 
> > Tim
> > 
> > On Mon, 28 Nov 2005, Kristen Lindgren wrote:
> > 
> > > Hello.  Sorry for the recent onslaught of e-mails, but I'm just
> > getting into
> > > DTI analysis and I'm very excited to finally get going.  I've been
> > following
> > > the walk-throughs and tutorials on the website for FDT, but I keep
> > getting
> > > the same error when I run DTIFit (child killed: SIGABRT).  Here's
what
> > I've
> > > done so far just to make sure that I haven't missed something
(FYI,
> > I'm
> > > using Mac OS X Version 10.4.3):
> > Â> 
> > > 1) Processed 4D diffusion weighted dataset (b0 and 15 directions)
> > using
> > > "Eddy Current Correction" -> Created data.hdr and data.img file
> > > 
> > > 2) Based on instructions given in an archive e-mail, I created the
> > nodif and
> > > nodif_brain_mask files
> > > -Make a nodif file from this using the following command:
> > > avwroi corrected_file_name nodif 0 1
> > > -Remove the skull from this image using:
> > > bet nodif nodif_brain
> > > -Check that this has worked using:
> > > slices nodif nodif_brain
> > > -Make the brain image into a binary mask using:
> > > avwmaths nodif_brain -bin nodif_brain_mask
> > > 
> > > 3) Created bvecs and bvals files.  I normalized the values in
bvals
> > based on
> > > the formula in the FAQ.
> > > 
> > > 4) Ran DTIFit from the fdt_gui.  I tried this two ways: 1) letting
FDT
> > > automatically select the files and 2) manually selecting the
files.
> > Both
> > > yielded the same error.
> > > 
> > > Any thoughts on why this is happening?  Thanks!
> > > 
> > > Kristen
> > > 
> > 
> > 
> 
> 

-- 
 Stephen M. Smith  DPhil
 Associate Director, FMRIB and Analysis Research Coordinator

 Oxford University Centre for Functional MRI of the Brain
 John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
 +44 (0) 1865 222726  (fax 222717)

 [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve