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Dear Jessie, If your labels are wrong then you definitely need to fix the data before doing anything else. It is a *very* good thing that you have a marker (Vit E) to distinguish left from right. The tools you need to use to fix your orientation problem are fslswapdim and fslorient. I recommend the following strategy: take a copy of your original data fslorient -deleteorient copiedimage fslswapdim copiedimage y -x z reorientedimage where "y -x z" is just an example. You need to work out what the right options are here so that it makes your image look like one of the template images (look at any of the standard images in FSLView). Ignore any warnings about left-right swapping, as you may need to force this to happen in order to fix the problem. (For example, if it is only the left-right which seems swapped then "-x y z" are the right options) Once it looks correct in FSLView (showing the L label and the Vit E marker on the right side of the transverse/axial view) then do: fslorient -setsformcode 1 reorientedimage fslorient -forceradiological reorientedimage If you then look at this image in FSLView you should see the labels in the correct places. I hope this helps. All the best, Mark P.S. It is usually much nicer to avoid all of this by finding a converter to nifti that gets things correct first time. I recommend mricron's dcm2nii or FreeSurfer's mri_convert, but there are many other options out there too. Have a look and see if you can find a better one that you are currently using. On 21 Dec 2009, at 19:11, Jessie Mathews wrote: > Hello, > > I am following up with my question that was posted a few weeks ago. > Given the labels > below on FSL view, what does this mean for our data? > > Regards, > > J. > > On Fri, 4 Dec 2009 09:51:11 -0800, Jessie Mathews <[log in to unmask] > > > wrote: > >> Hi Dave, >> >> Here are where the labels are placed for all views: >> >> Coronal: R on left, L on right, S on top, I on bottom >> >> >> Sagittal: P on left, A on right, S on top, I on bottom >> >> >> Transverse: R on left, L on right, A on top, P on bottom >> >> >> Thank you, >> >> >> Jessie >> >> On Fri, Dec 4, 2009 at 12:22 AM, Dave Flitney >> <[log in to unmask]>wrote: >> >>> Sorry Jessie, meant to ask where fskview places all the labels? >>> Never >>> e-mail before your first coffee! >>> >>> >>> Dave Flitney, IT Manager >>> University of Oxford, FMRIB Centre >>> JR Hospital, Oxford OX3 9DU >>> T: 01865 222713 F: 01865 222717 >>> >>> On 4 Dec 2009, at 08:18, Dave Flitney <[log in to unmask]> >>> wrote: >>> >>> Jessie, >>>> >>>> Just to comfirm the rest of the acquisition orientation: in >>>> fslview where >>>> does it place the A&P labels? >>>> >>>> Dave Flitney, IT Manager >>>> University of Oxford, FMRIB Centre >>>> JR Hospital, Oxford OX3 9DU >>>> T: 01865 222713 F: 01865 222717 >>>> >>>> On 3 Dec 2009, at 19:47, Jessie Mathews >>>> <[log in to unmask]> wrote: >>>> >>>> Dear FSL Experts, >>>>> >>>>> Our data is currently in neurological orientation, as confirmed >>>>> by a >>>>> Vitamin E capsule (we >>>>> placed the Vit. E pill on the left side of the head and fslview >>>>> shows the >>>>> pill on the left side >>>>> of the screen). >>>>> >>>>> Using fslorient -getorient, however, fsl thinks that our data is >>>>> in >>>>> radiological orientation. >>>>> Additionally, the labels in fslview show the opposite from what >>>>> they >>>>> should - the left side is >>>>> labelled as right. >>>>> >>>>> How does this effect my interpretation of data? Can I simply >>>>> just swap >>>>> left for right in my >>>>> results? For example, switch positive x coordinates with >>>>> negative ones? >>>>> Or are my results >>>>> uninterpretable as is. Please let me know if there is a solution >>>>> for >>>>> this. >>>>> >>>>> Thank you in advance. >>>>> >>>>> >>>> >> >