Funny, I checked example_func in tkmedit like you said, and it looks fine.
Attached are screenshots of that and the initial registration.  Sorry the
tkmedit window is a little distorted, it got squished when I pasted it into
paint.   After fixing it in tkregister2 the overlay looks correct (compared to
how it looks in fslview) but let me know if you think there might have been a
glitch somewhere in the whole process that I don't know about..I'm just
suspicious because, like you said, I shouldn't have had to adjust so much.
I'll have to do this later with other subjects, I'll email again if it happens
again.  Thanks for your help Doug.

Stacy

Quoting Doug Greve <greve@nmr.mgh.harvard.edu>:

  

No, you should not need to do that much adjustment. Is this a full or
partial volume?

It could be that your nifti volume is oriented incorrectly. To check this,

tkmedit -f example_func.nii

Make sure that the different cardinal views are oriented correctly.

doug

Stacy Chu wrote:

    

Thanks, I actually ended up finding that SagMir button and after playing
      

around
    

with it I got it to fit the surface.  By lowering the intensity and
      

comparing
    

the fit between the two hemi's in the sagittal view it became obvious which
      

one
    

fit better.  The orientation was initialy completely upside down and flipped
      

the
    

wrong way.  Is it very uncommon to need to adjust so much?  What could be
      

the
    

reason?  I am using nifti.

Stacy

Quoting Doug Greve <greve@nmr.mgh.harvard.edu>:



      

You can't really do a left-right flip in tkregister2. ok, you can with
"Sag Mirror", but I would *highly* recommend that you find out whether
you really need one or not and, if so, why. LR orientation can be tricky
to determine, even within the same subject. Are you using nifti?



Stacy Chu wrote:



        

Hi all,

I used

reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
--subject
          

FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
    

and then

reg-feat2anat --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat
--subject
          

FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
    

--manual

to register and edit the registration of a functional to its anatomical


          

volume.


        

The initial registration came out pretty bad and I think I need to do a
left-right flip.  I see that I can rotate/translate/resize using


          

tkregister2,


        

but I can't figure out how to make a flip.  Does anyone know the best way
          

to
    

do


        

that?  If the registration looks so bad do I need to change something in
          

the
    

command for my initial registration process?  Thanks!

Best,

Stacy

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



    

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---

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting