When I type

tkregister2 --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat

I get an error message saying ERROR: Option --feat unknown

I also did the second check you recommended and it looks good.  But I just
realized - and this could be why it came out fine when I checked example_func
in tkmedit - I already fixed the registration using tkregister2.  I dont know
why I didn't realize this before.  example_func.nii would get corrected when I
save changes, no?  So maybe it was just that the nifti volume was oriented
incorrectly?

By the way, could I ask you to check the .gfeat problem I ran into when you get
a chance?  I sent it to the mailing list.  Thanks very much for all your help!

Stacy

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

  

Out of curiosity, how does the registration to standard space look?
Check it with:

tkregister2 --feat istlevel_FWIO_fmri_NYU_KB_Nov30_06_epi1swap_z2_3.feat

You can also look at the initial func-struct registration with:

tkregister2 --mov example_func.nii --s
FREESURFERRECON_FWIO_fmri_NYU_KB_Nov30_06_20061130.095534.281000_1
 --regheader --reg /tmp/junk

This will likely be way off, but it should get things more or less lined
up (to within 45degrees rotation), if not, then that's a problem.

doug


Stacy Chu wrote:

    

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

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer








              

--
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








            

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.






          

--
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





        

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.



------------------------------------------------------------------------

      

--
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



    

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.


  

-- 
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