Hi,

If your labels are not correct in the original scans then you should
not do any analysis until this is fixed.  Never try and fix this after
any analysis.

If your AP labels are incorrect in your original functional scans then
I recommend trying to reconstruct to the nifti format with another
piece of software.  You can try and use fslswapdim to fix the AP
labels, but unless you have a vitamin E capsule or some other form
of marker in the image, you will never be sure whether left and right
are the correct way around.  The best solution is to try and get the
conversion software to extract this information from the raw images
as these raw images (in manufacturer's formats or DICOM) always
contain the relevant orientation information.  Internally we use the
dcm2nii tool from mricron and find that it works very well, but there
are several other tools out there including a very good one from
FreeSurfer (mri_convert).

All the best,
	Mark



On 1 Dec 2009, at 00:08, Shal Hat wrote:

> Hi Mark,
>
> I know I kind of beat this issue to death. I have my AP labels  
> mismatching the actual functional hdr files.
> So does that mean that in FSL RL are also mismatched, and therefore  
> the R is actually not Right in the
> stats..
>
> Thanks !
>
> On Mon, Nov 30, 2009 at 3:14 AM, Mark Jenkinson  
> <[log in to unmask]> wrote:
> Hi Again,
>
> The R does not move up or down in the images.
> It will move from side to side, depending on which is Right!
>
> I assume that your registration issues are dealt with in the
> subsequent emails, so I will not comment on them further
> in this thread.
>
> All the best,
>        Mark
>
>
>
> On 28 Nov 2009, at 22:53, Shal Hat wrote:
>
> Thanks Mark,
>
> Regarding R, is it always placed in the same position of the screen,  
> or does it change according to the orientation
> of the brain (frontal lobe down vs. frontal lobe up)?
>
> Also, there seems to be an issue with registration that is more  
> pronounced using talariach labels (2mm) than MNI152.
> The anatomical axis registration seems to be mixed up in the output  
> file. The coronal slices are outlined (in red) by the
> saggital registration atlas/space, the saggital slices are outlined  
> (in red) by the axial registration atlas/space, and the
> axial slices are outlined (in red) by the coronal registration atlas/ 
> space.
>
>
>
> Thanks,
>
>
>
> On Sat, Nov 28, 2009 at 4:40 PM, Mark Jenkinson  
> <[log in to unmask]> wrote:
> Hi,
>
> If this is the same as your original functional image (in terms of
> orientation) then this is fine.  The R always means Right.  If you
> see the letter R on a sagittal slice then something is wrong with
> the orientation information in your nifti images.
>
> All the best,
>       Mark
>
>
>
> On 28 Nov 2009, at 17:01, *Shal Hat* wrote:
>
> Hi,
>
> after conducting a first level analysis, the post-stats result  
> provided anatomicals/SPM with
> frontal lobe facing down. It also had the letter R on one corner of  
> each image. Given this
> circumstance, does the R still signify Right?
>
> Thanks !
>
>
>