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.
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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