Hi again,
the registration looks fine in tkregister2, but is apparently wrong in fslview (and also mricron). See the attached files (as link from http://vedlegg.uib.no/?id=399ad2cce1a3138f8eb4f6a06f4acfc4) showing screenshots of fslview and tkregister2. How can this be explained, and how can we visualize the correct orientation in fslview? What does this misalignment influence any further processing with fnirt and concatenation of the affine transformation fields?
This is our command we run for bbregister:
bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat --init-fsl --t2 --o test.nii.gz
where vol0001 is the first volume in the fmri sequence and is flipped to align with LAS (as the highres).
Thank you for your kind help,
Erlend Hodneland
ean that it is in the wrong orientation? It should be in the same orientation as the anatomical. How does the reg look in tkregister2? Note that fslview can display volumes in odd orientations even when the orientation is correct. doug
On 04/13/2012 03:31 AM, Erlend Hodneland wrote:
Hi,
we are trying to register fmri FEAT data (example_func.nii) to the anatomical scan (processed in Freesurfer) using bbregister to opt. the affine registration before running FNIRT.
However, the orientation of the registered image is flipped around and is incorrect after applying bbregister.
We have tried:
- bbregister --s subj_501 --mov example_func.nii.gz --reg
register.dat --init-header --bold --o example_func2highres-fs.nii 2) bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-fsl --bold --o example_func2highres-fs.nii 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat "myfeatdirectory" 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat (this one looks correct) followed by bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-reg tkreg.dat --bold --o example_func2highres-fs.nii
reorienting to match the highres:
fslorient -swaporient example_func fslswapdim example_func x -y z example_func_swap (correct
orientation)
followed by bbregister --s subj_501 --mov example_func_swap.nii.gz --reg register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii
with the output being flipped in wrong orientation for all options.
We would greatly appreciate if you have any suggestions for how to overcome this problem!
Cheers/Sincerly/All best
Erlend Hodneland
Hi Erlend, while the images in the tkregister2 pics are oriented correctly the registration is way off. What images are you loading into fslview? You'll need to convert the orig.mgz into nii and load that to check the registration. doug
On 04/22/2012 04:16 AM, Erlend Hodneland wrote:
Hi again,
the registration looks fine in tkregister2, but is apparently wrong in fslview (and also mricron). See the attached files (as link from http://vedlegg.uib.no/?id=399ad2cce1a3138f8eb4f6a06f4acfc4) showing screenshots of fslview and tkregister2. How can this be explained, and how can we visualize the correct orientation in fslview? What does this misalignment influence any further processing with fnirt and concatenation of the affine transformation fields?
This is our command we run for bbregister:
bbregister --s subj_505 --mov vol0001.nii.gz --reg register-test.dat --init-fsl --t2 --o test.nii.gz
where vol0001 is the first volume in the fmri sequence and is flipped to align with LAS (as the highres).
Thank you for your kind help,
Erlend Hodneland
ean that it is in the wrong orientation? It should be in the same orientation as the anatomical. How does the reg look in tkregister2? Note that fslview can display volumes in odd orientations even when the orientation is correct. doug
On 04/13/2012 03:31 AM, Erlend Hodneland wrote:
Hi,
we are trying to register fmri FEAT data (example_func.nii) to the anatomical scan (processed in Freesurfer) using bbregister to opt. the affine registration before running FNIRT.
However, the orientation of the registered image is flipped around and is incorrect after applying bbregister.
We have tried:
- bbregister --s subj_501 --mov example_func.nii.gz --reg
register.dat --init-header --bold --o example_func2highres-fs.nii 2) bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-fsl --bold --o example_func2highres-fs.nii 3) bbregister --s subj_501 --o example_func2highres-fs.nii --feat "myfeatdirectory" 4) tkregister2 --mov example_func.nii --regheader --reg tkreg.dat (this one looks correct) followed by bbregister --s subj_501 --mov example_func.nii.gz --reg register.dat --init-reg tkreg.dat --bold --o example_func2highres-fs.nii
reorienting to match the highres:
fslorient -swaporient example_func fslswapdim example_func x -y z example_func_swap (correct
orientation)
followed by bbregister --s subj_501 --mov example_func_swap.nii.gz --reg register.dat --init-fsl --bold --o example_func_swap2highres-fs.nii
with the output being flipped in wrong orientation for all options.
We would greatly appreciate if you have any suggestions for how to overcome this problem!
Cheers/Sincerly/All best
Erlend Hodneland
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Erlend Hodneland