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Thankyou very much for the info David. I will try it and get back to you if get stuck. Aman On Wed, Aug 4, 2010 at 3:42 PM, David Gutman <[log in to unmask]> wrote: > In order to do anything with the bruker 2dseq files you need to use > MRICRO (not MRICRON) > > and use the File-->Open used header information (RAW) > > Then you need to give it the X,Y and Z dimensions (basically theMATRIX > which is something like 128x128 or whatever) and Z = number of slices > > and most likely.. also click the "Data 16-bit" and little:Endian > button (and make it Intel not Sun)... > > > Once you do that... you can "save" it as an analyze file so that FSL > can play with it.... just email me offline if you get super stuck... > > > > > On Wed, Aug 4, 2010 at 4:38 PM, aman gupta <[log in to unmask]> > wrote: > > Thanks Silviu for the reply. Actually, i have already tried converting > > these images to NIFTI using MRIcron using its dcm2nii utility, but it > didn't > > work. The problem i think is that the Bruker images are not exactly in > DICOM > > format but in some 2dseq format ( although the images don't show any .dcm > or > > any other extension), that's why i am having trouble with FSL accepting > > them. > > Aman > > > > On Wed, Aug 4, 2010 at 3:18 PM, Silviu Podariu <[log in to unmask]> > wrote: > >> > >> Aman, > >> > >> FSl works with NIFTI formats (type 'fslchfiletype' and see the output > for > >> what formats are allowed). > >> > >> Usually we convert DICOM to NIFTI using MRIcron's dcm2nii utility > (search > >> and install MRIcron, dcm2nii comes with it). So, first, you will have to > map > >> your data from Bruker to NIFTI somehow. > >> > >> Silviu > >> > >> -----FSL - FMRIB's Software Library <[log in to unmask]> wrote: ----- > >> > >> To: [log in to unmask] > >> From: aman gupta <[log in to unmask]> > >> Sent by: FSL - FMRIB's Software Library <[log in to unmask]> > >> Date: 08/04/2010 01:41PM > >> Subject: [FSL] FSL not accepting image format from Bruker > >> > >> Hi, > >> I am trying to run tractography on the DTI images obtained from Bruker > DRX > >> Avance imaging system using FSL, but i am having trouble with the image > >> formats. FSL is not accepting the image format from Bruker. Does anybody > >> else have faced this issue before? I would appreciate it if anyone could > >> provide some input on that? > >> > >> > >> Thanks,Aman Gupta > > > > > > > > -- > David A Gutman, M.D. Ph.D. > Center for Comprehensive Informatics > Emory University School of Medicine >