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Dear Sir, bet2 worked! Thanks! Swati Matt Glasser wrote: > You might need to use bet2 (which is now the regular bet in FSL 4.0). > > Peace, > > Matt. > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf > Of Swati Rane > Sent: Wednesday, October 31, 2007 11:35 AM > To: [log in to unmask] > Subject: Re: [FSL] error in dtifit > > Dear Sir, > > I could not find the -z option in the BET options. Am I missing > something here? > (I am using FSL 3.3) > > Swati > > Steve Smith wrote: > >> have you tried -Z option in BET? >> >> >> >> On 31 Oct 2007, at 14:07, Swati Rane wrote: >> >> >>> Dear Sir, >>> >>> I generated the input masks using the following 2 commands: >>> >>> avwroi data_4D nodif 0 1 >>> bet nodif nodif_brain -m -f 0.1 >>> >>> data_4D is my 4D data generated using the command 3dto4d. >>> I use a lower threshold of 0.1 because my images have low SNR. >>> The 4D data is fine, nodif shows all 3 slices but not odif_brain and >>> nodif_brain_mask. >>> >>> Swati >>> >>> Tim Behrens wrote: >>> >>>> How have you generated the input mask? It should be derived from the >>>> original data, and therefore have the same number of slices. >>>> >>>> T >>>> >>>> >>>> On 29 Oct 2007, at 14:08, Swati Rane wrote: >>>> >>>> >>>>> Dear Sir, >>>>> >>>>> I am not sure if this is what you wanted to know. I checked the >>>>> nodif_brain and nodif_brain_mask which indeed have only 2 slices >>>>> (nodif has 3 slices). How do I fix that if that is the problem? >>>>> I do not know hot to check if the 'littlebit' option is set. Could >>>>> you please let me know? >>>>> >>>>> Thanks! >>>>> >>>>> Swati >>>>> >>>>> >>>>> >>>>> Saad Jbabdi wrote: >>>>> >>>>>> Hi Swati, does it output 3-slice files with the first slice empty, >>>>>> or just 2-slice files? >>>>>> in the second case, the only way it could happen is: >>>>>> - your input mask has only 2 slices >>>>>> - you have set the --littlebit option >>>>>> >>>>>> could you check if one of these two is true? >>>>>> >>>>>> saad. >>>>>> >>>>>> >>>>>> On 28 Oct 2007, at 21:39, Swati Rane wrote: >>>>>> >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> The input to dtifit seems OK. Also I made a mistake. It actually >>>>>>> shows the last 2 slice not the first slice i.e. slice no. 1 and 2 >>>>>>> but not slice 0. >>>>>>> >>>>>>> Swati >>>>>>> >>>>>>> Tim Behrens wrote: >>>>>>> >>>>>>>> Hi - is it possible that it has processed all three slices, but >>>>>>>> when you look at it in fslview, the highest slice number is 2? >>>>>>>> If this is the problem, then I think it will be because fslview >>>>>>>> starts counting at 0 and not at 1, so slice 2 is actually the >>>>>>>> 3rd slice. >>>>>>>> >>>>>>>> T >>>>>>>> On 27 Oct 2007, at 10:56, Steve Smith wrote: >>>>>>>> >>>>>>>> >>>>>>>>> Hi - if you look at all timepoints of all slices of the data >>>>>>>>> output by eddy_correct do they look ok? I.e., is the input to >>>>>>>>> dtifit ok? >>>>>>>>> >>>>>>>>> Cheers. >>>>>>>>> >>>>>>>>> >>>>>>>>> On 26 Oct 2007, at 17:39, Swati Rane wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hello, >>>>>>>>>> >>>>>>>>>> I use the older version of FSL (3.3). When I use the dtifit >>>>>>>>>> command for my 3 >>>>>>>>>> slice data, the display says that it has processed all 3 >>>>>>>>>> slices, but when I >>>>>>>>>> look at the FA map in FSL view, I can see only the last 2 >>>>>>>>>> slices. Can you >>>>>>>>>> tell me what is the error in my processing? >>>>>>>>>> >>>>>>>>>> Thanks! >>>>>>>>>> >>>>>>>>>> Swati >>>>>>>>>> >>>>>>>>> >>>>>>>>> > --------------------------------------------------------------------------- > >>>>>>>>> Stephen M. Smith, Professor of Biomedical Engineering >>>>>>>>> Associate Director, Oxford University FMRIB Centre >>>>>>>>> >>>>>>>>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >>>>>>>>> +44 (0) 1865 222726 (fax 222717) >>>>>>>>> [log in to unmask] <mailto:[log in to unmask]> >>>>>>>>> http://www.fmrib.ox.ac.uk/~steve >>>>>>>>> >>>>>>>>> > --------------------------------------------------------------------------- > >>>>>>> -- >>>>>>> ___________________________________________________________________ >>>>>>> Swati D. Rane >>>>>>> Ph.D. candidate (Bioengineering) Department of >>>>>>> Biomedical Engineering Lab: Yerkes Imaging Center >>>>>>> Georgia Institute of Technology Emory University >>>>>>> Email: [log in to unmask] >>>>>>> <mailto:[log in to unmask]> Phone: 404 712 9109 >>>>>>> >>>>>>> Webpage: http://www.prism.gatech.edu/~gth780f/ >>>>>>> <http://www.prism.gatech.edu/%7Egth780f/> >>>>>>> ___________________________________________________________________ >>>>>>> >>>>>> > --------------------------------------------------------------------------- > >>>>>> 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] <mailto:[log in to unmask]> >>>>>> http://www.fmrib.ox.ac.uk/~saad <http://www.fmrib.ox.ac.uk/%7Esaad> >>>>>> >>>>>> > --------------------------------------------------------------------------- > >>>>>> >>>>>> >>>>>> >>>>>> >>>>> -- >>>>> >>>>> ___________________________________________________________________ >>>>> Swati D. Rane >>>>> Ph.D. candidate (Bioengineering) Lab: Yerkes Imaging Center >>>>> Georgia Institute of Technology Emory University >>>>> Email: [log in to unmask] Phone: 404 727 5541 >>>>> >>>>> Webpage: http://www.prism.gatech.edu/~gth780f/ >>>>> ___________________________________________________________________ >>>>> >>> -- >>> >>> ___________________________________________________________________ >>> Swati D. Rane >>> Ph.D. candidate (Bioengineering) Lab: Yerkes Imaging Center >>> Georgia Institute of Technology Emory University >>> Email: [log in to unmask] Phone: 404 727 5541 >>> >>> Webpage: http://www.prism.gatech.edu/~gth780f/ >>> ___________________________________________________________________ >>> >> >> > --------------------------------------------------------------------------- > >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve >> >> > --------------------------------------------------------------------------- > > > > -- ___________________________________________________________________ Swati D. Rane Ph.D. candidate (Bioengineering) Lab: Yerkes Imaging Center Georgia Institute of Technology Emory University Email: [log in to unmask] Phone: 404 727 5541 Webpage: http://www.prism.gatech.edu/~gth780f/ ___________________________________________________________________