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