Hi John,
I would use the ApplyXFM GUI for this task (with the identity transformation and selecting "Voxel Dimensions" for the output size) as it should give you the control you want and should deal correctly with the orientation and geometry information.
All the best,
Mark
> On 22 Oct 2018, at 23:45, John Guige <[log in to unmask]> wrote:
>
> Hello,
>
> I hope everyone is well! I am hoping to get some help on an issue I am having with the outcomes of my FLIRT registration.
>
> So, for the past few weeks (I work as an undergraduate in the lab I am in), I have been working on trying to adjust dimensions/voxel sizes for a brain mask. I have the mask, but I want it fit to certain dimensions and voxel sizes. My mask dimensions are 182x218x189. I want to get them down to 79x95x79.
>
> After looking around quite a bit, I found the best way to do this was to use FLIRT. My only issue was that I did not have a reference image I could use for the registration. After doing some more searching, I came across the tool “fslcreatehd”, which allowed me to create a NifTi image with the dimensions that I wanted.
>
> Before trying to run FLIRT to align my mask with a 79x95x79 image, I successfully tried the following with a 91x109x91 goal.
>
> I used “fslcreatehd” to make an image with all the same parameters as my input image except for the voxel dimensions, which were 91x109x91.
>
> I ran my input image and the reference image through FLIRT, and it worked great! Upon opening the image in FSLeyes, everything looked like it worked.
>
> I then tried the same above, but this time, using flscreatehd to make an image with 79x95x79 dimensions.
>
> Using fslinfo, I saw that the output image had what I desired. But when opening it in FSLeyes, something very strange occurred. When I first open it up, nothing is there when the cursor is on the center. No image intensities at all. Here is an image of what it looked like upon opening:
>
> https://imgur.com/a/lxpWi6r
>
> So I moved my cursor around, trying to see if there were any intensities at all, and turns out, in the bottom left, there were. Here are a few images of what it looks like when I have my cursor down there:
>
> Image 1:
> https://imgur.com/a/86EEAeR
>
> Image 2:
> https://imgur.com/a/Bxjr5NF
>
> Image 3:
> https://imgur.com/a/ajiINwf
>
> It seems to me the orientation may be off, and that the image was moved over quite a bit? I am really not sure what happened. While I know the voxel dimensions changed how I wanted them to, I am still not sure as to what I can do so the image is not oriented/moved the way it is. Can anyone help? Might it be the specific voxel dimensions I am trying to use? I know that 79x95x79 may not be a very common dimension usage, but I am not sure why that would cause my entire image to move to like it has.
>
> Any help or advice would be greatly appreciated! Thank you!!
>
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