Hello,

> 1.  To follow-up on "spaces," how does one know the appropriate  
> display range in FSLview for the different images?

Look at the intensities that are contained in the image.  Either click
around different voxels in FSLView and note the values in the
"intensity" box (near the coordinate displays) or use a tool like
"fslstats" with the -r (or -R) option.  When you have a feeling for
the range of intensity values, just set the display range (min and max)
in FSLView to cover this range (and not much more).

>
> 2.  To follow up on the registration --
>
> 	a.  Is it possible to register a FIRST hippcampus (already  
> segmented & boundary corrected) to standard space?
> 	e.g.,
>
> 	flirt -in [FIRST hippocampus; segmented & boundary corrected] -ref  
> [MNI152_T1_2mm] -out [name] ?

You should not do this.  You should only register images that look
like each other (e.g. the image of a whole brain and another image
of a whole brain, not of one isolated structure).  However, if you have
run FIRST then the registration has already been done and saved
in a file called something like *_to_std_sub.mat
You can *apply* this transformation (the result of a registration) to
any image in the original space using the -applyxfm flag in FLIRT.

> 	What is the appropriate display range for this image?

For a labeled image it will depend on the structure with the maximum
label number.  Typically if you set the range to be 0 to 40 then you
should see things fine.  But use the strategy I describe above to know
for sure.

> 	b.  Or must one perform the flirt registration to standard space  
> from the raw structural image with no brain extraction?  And then  
> use FIRST to segment the desired hippocampus?

If you use run_first_all then this is all done for you.  And yes, it  
is recommended
to use non-brain-extracted images with this.

All the best,
	Mark



>
> Thank you.  Very much.
>
>
> On Sat, Nov 28, 2009 at 3:35 PM, Mark Jenkinson  
> <[log in to unmask]> wrote:
> Hello,
>
> There is no real reference about "spaces" besides the documentation.
> I'll try to answer your questions:
>
> 1 - Outputs are in different spaces as the originally acquired images
>        are in different spaces.  That is, the Field Of View (FOV) and
>        resolution are different for the functional, structural and
>        standard/template images.  We try to keep things in the most
>        appropriate space, partly because moving between spaces
>        involves registration and resampling steps which can be  
> inaccurate
>        and the interpolation (in the resampling) will degrade the  
> image
>        quality by some amount.
>
> 2 - As examples:
>        Functional images might be 64x64x40 voxels with 3x3x4mm  
> resolution
>        Structural images might be 256x256x200 voxels with 1x1x1mm  
> resolution
>        Our standard space template images are 91x109x91 voxels with  
> 2x2x2mm resolution
>
> 3 - The spaces correspond to your different acquisition images - so  
> just check
>        by comparison with your original images.
>
> For your registration I'm not sure what your [FIRST INPUT] image  
> is.  Is it a
> structural image with no brain extraction?  If so, then you should  
> not register
> to the avg152T1_brain but use the non-brain extracted version.   
> Also, we
> recommend sticking with the MNI152 naming, so MNI152_T1_2mm would
> be the appropriate image in this case.  I am not sure what you mean by
> "appropriate brain region".  Also, check that the display range is  
> set appropriately
> in FSLView, as having this range set badly (which sometimes happens
> with the default settings) could make the whole image look white.
>
> All the best,
>        Mark
>
>
>
> On 28 Nov 2009, at 17:10, ACE . wrote:
>
> Hello.
>
> Could you please point me to a resource about different "brain  
> space" options? (e.g., high resolution space; standard space; native  
> space?)
>
> I have read the registration information on the FSL website, but I  
> have additional questions such as the following:
>
> 1.  Why are different FSL outputs in different spaces?
>
> 2.  Could you give me an example of a FSL image in each "space?"
>
> 3.  What is the best way to determine an image's "space?"  Is there  
> a list of which voxel dimensions signify which "space?"
>
> To register a FIRST brain area (with boundary correction) to  
> standard space -- I tried the following command:
>
>  flirt -in [FIRST INPUT] -ref avg152T1_brain -out [name]
>
> But I do not see the appropriate brain region in FSLview when I open  
> the output.  I see "white" throughout the entire brain.  Any thoughts?
>
> THANK YOU.
>
>
>