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Hi Mark, By single-voxel data I was referring to single-voxel MRS data. For our application, we need to tissue segment triple-obliqued 30 x 20 x 10 mm voxels that were positioned within the hippocampus. Following the initial BET, I checked the header information and indeed there is valid qform information (qform_code = 2). Would be able to point my in the right direction from here in terms of pulling out an arbitrary obliqued ROI? Please let me know if you need additional information. Many thanks, Andy Mark Jenkinson wrote: > Hi Andy, > > I'm not sure what you want here, or precisely what "single-voxel data" > is. > You can represent any arbitrary ROI using a mask image and that's what > I would recommend. The difficulty is knowing how the axes of the two > images relate to each other. Have your images been converted to > nifti, and if so, do they contain valid qform information (use fslhd and > see if the qform_code is non-zero). If so then we can probably do this > using the qform information. If not, you'll have to figure out some way > of relating the images together. > > If this isn't quite what you were after, then please send us a more > detailed description of your situation. > > All the best, > Mark > > > > On 21 Mar 2008, at 17:35, Andy Prescot wrote: > >> Hi, >> >> I need to tissue-segment triple-obliqued single-voxel data that were >> planned >> using non-obliqued T1w images (Varian Unity/INOVA data). >> >> For non-obliqued single-voxel data I perform a BET, FAST, fslroi to >> extract >> the 'segmanted' voxel, and obtain the tissue contributions from the >> resulting histogram. Is there a way to extract arbitrarily >> shaped/obliqued >> segmented roi's using FSL? Maybe there is a way to oblique the >> orthogonal >> ax/cor/sag planning images to match the three single-voxel rotations and >> then segment using my standard method?? >> >> Many thanks in advance for any assistance. >> Andy >> > > The information transmitted in this electronic communication is > intended only > for the person or entity to whom it is addressed and may contain > confidential > and/or privileged material. Any review, retransmission, dissemination > or other > use of or taking of any action in reliance upon this information by > persons or > entities other than the intended recipient is prohibited. If you > received this > information in error, please contact the Compliance HelpLine at > 800-856-1983 and > properly dispose of this information. > > > > > -- ***************************************************** Andrew P. Prescot, Ph.D. Dept. of Psychiatry, Harvard Medical School Brain Imaging Center, McLean Hospital 115 Mill St., Belmont, MA, 02478 (617) 855 2676 Fax (617) 855 2770 *****************************************************