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Hi Lino - I think the problem is a simple one. The file with the data in in your directory must be called data.* in your directory, it is called orig_data.nii.gz so bedpost does not know where the data is. You could have found this out by running bedpost_datacheck on the directory. I am sorry not to have suggested this earlier, but I assumed that you had used the default settings for dtifit, so this couldn't be the problem. I guess you actually selected the dtifit input files manually? At least it will be easy to fix! Cheers 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 [log in to unmask] www.fmrib.ox.ac.uk/~behrens On 9 Feb 2006, at 18:52, lino becerra wrote: > thanks Tim, it's called lino_dti.tar.gz > > Lino Becerra PhD > Co-Director > P.A.I.N. Group > Brain Imaging Center > McLean Hospital > 115 Mill St. > Belmont, MA 02478 > Ph: 617-855-2475 > Fﾂ : 617-855-3772 > > > On Feb 9, 2006, at 12:16 PM, Tim Behrens wrote: > >> OK - I guess this isn't the problem.ﾂ >> Can you tar up you input directory, and upload it onto the FMRIB >> upload >> www.fmrib.ox.ac.uk/cgi-bin/upload.cgi >> >> I'm afraid I won't be able to look at it until mid next week as I >> am going away, but I will do it as soon as I get a chance. >> >> 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 >> >> [log in to unmask] >> www.fmrib.ox.ac.uk/~behrens >> >> >> >> >> >> On 9 Feb 2006, at 16:49, lino becerra wrote: >> >>> yes, i run dtifit and the resulting images (fa, L1, etc) are fine >>> >>> Lino Becerra PhD >>> Co-Director >>> P.A.I.N. Group >>> Brain Imaging Center >>> McLean Hospital >>> 115 Mill St. >>> Belmont, MA 02478 >>> Ph: 617-855-2475 >>> Fﾃつ : 617-855-3772 >>> >>> >>> On Feb 9, 2006, at 11:50 AM, Tim Behrens wrote: >>> >>>> can fslview read your data properly? >>>> >>>> T >>>> >>>> >>>> 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 >>>> >>>> [log in to unmask] >>>> www.fmrib.ox.ac.uk/~behrens >>>> >>>> >>>> >>>> >>>> >>>> On 9 Feb 2006, at 16:33, lino becerra wrote: >>>> >>>>> Hi Tim: >>>>> The diff_slices directory wasn't created >>>>> I just run bedpost_datacheck abd found that the datatype of my >>>>> data is 4, it should be 16. >>>>> Do you think this could be part of the problem?ﾃδづつ >>>>> thanks >>>>> lino >>>>> Lino Becerra PhD >>>>> P.A.I.N. Group >>>>> Brain Imaging Center >>>>> McLean Hospital >>>>> 115 Mill St. >>>>> Belmont, MA 02478 >>>>> Ph: 617-855-2475 >>>>> Fﾃδづつ : 617-855-3772 >>>>> >>>>> >>>>> On Feb 9, 2006, at 11:26 AM, Tim Behrens wrote: >>>>> >>>>>> Hiya - what is the result of >>>>>> >>>>>> ls -l <subjdir.bedpost>/diff_slices/*/thsamples.* |wc -l >>>>>> is it the same as the number of slices? >>>>>> >>>>>> if so, what is the result of avwinfo on one of those files >>>>>> >>>>>> e.g. >>>>>> >>>>>> avwinfoﾃδづつ <subjdir.bedpost>/diff_slices/data_slice0030/ >>>>>> thsamples >>>>>> >>>>>> 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 >>>>>> >>>>>> [log in to unmask] >>>>>> www.fmrib.ox.ac.uk/~behrens >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 9 Feb 2006, at 15:50, lino becerra wrote: >>>>>> >>>>>>> Hi: >>>>>>> I've been trying to run bedpost and after completion a >>>>>>> window pops up with a message: >>>>>>> error writing slice 0. writing slice 1..... >>>>>>> It seems that all the images are created but when I check >>>>>>> merged_thsamples it only has one volume >>>>>>> meanfsamples looks fine though. >>>>>>> Thanks! >>>>>>> lino >>>>>>> Lino Becerra PhD >>>>>>> P.A.I.N. Group >>>>>>> Brain Imaging Center >>>>>>> McLean Hospital >>>>>>> 115 Mill St. >>>>>>> Belmont, MA 02478 >>>>>>> Ph: 617-855-2475 >>>>>>> Fﾃδεつづδづつ : 617-855-3772 >>>>>>> >>>>>>> >>>>>>> Any information, including protected health information >>>>>>> (PHI), transmitted in this email is intended only for the >>>>>>> person or entity to which it is addressed and may contain >>>>>>> information that is privileged, confidential and/or exempt >>>>>>> from disclosure under applicable Federal or State law. Any >>>>>>> review, retransmission, dissemination or other use of or >>>>>>> taking of any action in reliance upon, PHI by persons or >>>>>>> entities other than the intended recipient is prohibited. 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