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Thank you, Mark! It's very clear! Thank you for your patient and helpful explanation. Mingxia On Sun, May 19, 2013 at 11:26 PM, Mark Jenkinson < [log in to unmask]> wrote: > Hi, > > 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? > > > No, not really. What fslswapdim does is to swap the data around. > However, if you are looking at one particular point of the anatomy then > that is equivalent to its coordinate changing. It is the voxel coordinates > that are swapped though, so there is no guarantee that -1 1 1 would become > 1 1 1 with a -x y z swap unless the mm coordinates (as these must be mm > coordinates, since voxel coordinates are always positive) are perfectly > arranged to have x=0 at the exact centre of the volume. > > (2) You agreed with Sourena's method, right? > fslswapdim orig_t1 -x y z flipped_t1 > fslswapdim orig_mask -x y z flipped_mask > > > Yes, in the sense that this will flip the general sense of left and > right, but it won't generally create images which can be neatly overlaid at > this point. That requires an extra registration step. > > 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? > > > I believe that we were talking about the orig_t1 being a T1 structural > image, not in standard space (as you wrote about "the T1 image" which > sounded more like a structural image of a single individual rather than an > image in standard space image). > > If all your images are in standard space then this is a special case and > not what I think we were talking about to start with. Only with the > standard space images can you avoid this registration step because in this > case the anatomy is aligned with the axes and x=0 is exactly at the centre > of the volume. So only in this case does the fslswapdim command with -x y > z produce a flipped image that requires no further processing. > > 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？ > > > Again, it was unclear before that everything was in standard space. If > so then you can just use fslswapdim and avoid the extra registration. > > 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? > > > No, I was referring to the case of an individual structural image, prior > to it being transformed into standard space. When not in standard space > then orientation of the head in the image is unlikely to be exactly aligned > with the axes (even if the radiographer tries to set this up in the slice > prescriptions). Hence the flipped usually creates a change in the tilt or > position of the head. In standard space it does not and you do not need to > worry about this. > > All the best, > Mark > > > > > 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 >>> > >>> >> >> >> > >