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Thanks to Tim, Matt and Andreas....I have dtifit working for my diffusion weighted brain images. I am now trying to do the same thing for some synthetic data sets, which is proving more difficult.........particularly generating the Bet mask....the shape of the synthetic data sets....spirals etc, seems to confuse the algorithm, I think.....so the resulting mask doesn't look like what is needed. Any way around this? Maybe generating a mask with only 1s? Is that possible? Thank you. Roger Matt Glasser wrote: > Hi, > > One thing that can cause this is if you don't have a carriage return at the > end of your last bvecs and bvals lines. > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf > Of Roger Moore > Sent: Wednesday, August 22, 2007 7:41 AM > To: [log in to unmask] > Subject: Re: [FSL] AW: [FSL] using dtifit > > Hi Tim and Andreas, > > Your suggestions have helped me make progress, but still not there yet. > > I can run dtifit no problem with the same command line as before: > > 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 > > and it processes all the slices. > > The problem is when I view them using fslview, there is nothing > there....just black. > > Any further suggestions? > > Andreas mentioned that the data and mask files are not in the same > directory as the dtift....is it really necessary that they are? I do not > seem to have permission to copy or move anything to that directory. > > Thank you for your help. > > Roger > > > > > > Tim Behrens wrote: > >> 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 >>> >>> > --------------------------------------------------------------------------- >