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Dear Mark,

I have thought this for a long time, but I still can not understand this. I have some questions about fslswapdim

(1) Take an easy example: If only one voxel in the mask and the coordinate is -1 1 1, when I used fslswapdim orig_mask -x y z output_mask, the coordinate of the output_mask would become 1 1 1, right?

(2) You agreed with Sourena's method, right? 
fslswapdim orig_t1 -x y z flipped_t1
fslswapdim orig_mask -x y z flipped_mask

Use flirt with 6DOF to register flipped_t1 into orig_t1, and apply the transformation matrix to your flipped_mask.

A. Specifically, what's the orig_t1? The mask is from the group level results which have been registered to MNI152_T1_2mm_brain.nii.gz, so the orig_t1 is MNI152_T1_2mm_brain.nii.gz?

B. How to apply the transformation matrix to your flipped_mask? Should I use flirt or applywarp? What's the input and reference? Again, the mask has been registered to standard T1, why register it again？

C. When you said "There's no reason that the mid-saggital plane of the T1 image should be aligned with the yz-plane at the mid-point on the x-axis.", you mean because the brain is not symmetrical? 

Thanks so much.

Mingxia


On Fri, May 10, 2013 at 9:54 AM, Mark Jenkinson <[log in to unmask]> wrote:
Hi,

There's no reason that the mid-saggital plane of the T1 image should be aligned with the yz-plane at the mid-point on the x-axis.  The chances are that this flip will also change the orientation and translation.  So you do need to do the registration.

All the best,
Mark


On 10 May 2013, at 07:19, zhang mingxia <[log in to unmask]> wrote:

Hi Sourena,

Thanks a lot. I tried:

 fslswapdim  orig_input -x y z flipped_output

Because the orig_input has been registered into the T1 image, I don't need to do further registration, right?

Mingxia


On Wed, May 8, 2013 at 8:48 AM, Sourena Soheili <[log in to unmask]> wrote:
Hi,
I have not done it before and others may have better ideas;but maybe it works:
swap left/right axis signs of both your original T1 and mask. If the
left/right axis is x it would be:
fslswapdim orig_t1 -x y z flipped_t1
fslswapdim orig_mask -x y z flipped_mask

Use flirt with 6DOF to register flipped_t1 into orig_t1, and apply the
transformation matrix to your flipped_mask.

Cheers,
Sourena

On 5/8/13, zhang mingxia <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I have a result in left hemisphere and want to investigate the laterality
> of this area. So, I planned to make a mask of this area then make the
> corresponding right side of mask based on the first mask and then extract
> the mean value of the two masks for further calculation.
>
> My problem is I don't know how to make the corresponding right side of mask
> based on mask in the left hemisphere. Hope to get some advice.
>
> Thanks in advance.
>
> Mingxia Zhang
>