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Hi Stefan - Can you check in fslview whether the diffusion-weighted volumes have lower signal intensity than the non-weighted ones. A problem tha I have come across before with data which has been processed with SPM is that SPM inserts a scale factor into the header ( I think it use the header variable called funused1 ) which then gets completely ignored by the FSL I/O routines.. Another way to check for this problem would be to run the following command on each of the 3D volumes output from SPM ( before the merge!): avwval volume funused1 This should be unset, or set to 1 in each case. If this is not the problem, then I would be happy to take a look at the data if you can tar it up and put it on an ftp site. Please do not email it. Thanks Tim ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- On Sun, 28 Nov 2004, [iso-8859-1] Stefan Klöppel wrote: > Dear Tim, > > thanks for the advice. I ran dtifit with spm-normalized data and received > only blank images (of around 30 kB each). When doing the same with ecc > volumes the error after slice 105 is 'child killed: SIGABRT'. The computer > has 3 GB swap Ram so I don´t assume problems from that directions. I also > checked pro recently described traps (e.g. UNIX carriage return). > > Any ideas? > > Stefan > > > -----Ursprüngliche Nachricht----- > Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]]Im Auftrag > von Tim Behrens > Gesendet: Dienstag, 23. November 2004 14:29 > An: [log in to unmask] > Betreff: Re: [FSL] No results with FDT Diffusion > > Dear Stefan - Have you run dtifit on this directory - this is always a > good check to make sure that everything in the directory is ok, as it only > takes a couple of minutes.. > > Tim > > > On Tue, 23 Nov 2004, Stefan Klöppel wrote: > > > Hi, > > I have been trying to compute DWI-data (60 directions, 6 B0 images 4 > > repetitions, 264 files) motion corrected and normalized with spm. I left > out > > the eddy current correction. I used avwmerge to generate the 4d volume and > > used the first B0-image as nodif-volume. There were no complaints by > > bedpost_datacheck. After 30 hours I viewed the outputs of bedpost and > found > > very distorted images, hardly recognisable as a brain. Consequently, when > > using probtrack, I received only blank images for every single seed voxel. > > > > When leaving out the whole pre-processing with spm but using fsl eddy > > current correction (ecc) and volume 1 as reference volume I receive the > > message: Both reference and input images have an sform matrix set (what > does > > it mean?) and ecc leaves me with a filesize below 1 MB (input data was > > 200MB). Using avwsplit to determine the bvecs (I assume that they are > > changed by ecc) produces nifti_read_buffer error. All extracted files > except > > the first are empty. > > I am stuck. Is there a way out. > > Thanks > > Stefan > > > > -- > ---------------------------------------------------------------------------- > --- > 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 > ---------------------------------------------------------------------------- > --- >