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
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