what different brain images do you mean? You can view them with the surfaces via:

tkmedit <subject name> norm.mgz lh.white -segmentation aparc+aseg.mgz

or

tkmedit <subject name> norm.mgz lh.white -segmentation aparc2009s+aseg.mgz

the tools will be part of FS 5.2 when it comes out in the next month or so. If you really need it before then Nick can get you a beta.

cheers
Bruce

On Sat, 1 Dec 2012, Assaf B. Spanier wrote:

Many thanks for the quick response -  I would take a look on your
suggestion!
How about my first question ? About viewing the segmentation results of my
first trial ( without the Flair images)

[Please forgive my English :) ]


On Sat, Dec 1, 2012 at 9:53 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Spanier

      definitely don't invoke recon-all with the FLAIR image. We have
      some tools in 5.2 for this, but you would call it as a
      postprocessing step with a different command line in any case.
      Instead, you can use bbregister to register the flair to the
      surfaces and resample it.

      cheers
      Bruce

      On Sat, 1 Dec 2012, Assaf B. Spanier wrote:

            Hi@all,
            I have a dataset of several MRI T1 images and one
            Flair. All images of the
            same subject and were taken in the same session.  My
            goal is to register and
            segment all those MRI images.
            = A =
            In my first try I have used, "recon-all -i image1 -i
            image2  etc'" for all
            T1 images (here, I didn't use the Flair images ) .
            Follow this, I used the
            "recon-all -all" command. (For about two days...) 

            Here come Question 1: After all this process, I
            didn't completely follow the
            results I got... As I have noticed that I have only
            one segmentation file
            (aparc.a2009s+aseg.mgz) ? How can I see the
            segmentation result
            with tkmedit in the different brain images ?

            = B =
            As I would like the neuroanatomical labels to be
            inspected for accuracy by a
            physician. My physician asks to see the segmentation
            result on top of the
            Flair images (saying it easier for him to do so on
            Flair images)
            So I've used the "recon-all -i image1 -i image2
             etc'"  command again
            but  this time I've also included the Flair image. 

            Here come Question 2:  However, this time,
            unfortunately, the  "recon-all -i
            image1 -i image2  etc'" ,  failed, saying that: 
            ~~~~~
            images have different voxel sizes.   Currently not
            supported, maybe first
            make conform? Debug info: size(1) = 0.5078, 0.5078,
            5.5   size(0) = 0.51,
            0.51, 5.5
            ~~~~~
            Is there something I can do to fix this ?

            Thanks for everyone involved in this great project!
            Highly appreciate your time and efforts.

            Best,

            Spanier








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