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
> >
>
>
--
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Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
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