Hi again
Yes, test.nii is the functional data registered to the anatomy.
The following files have now been uploaded to your filedrop and can be
downloaded by the email account "gr...@nmr.mgh.harvard.edu"
1. vol0001.nii.gz : functional input
2. orig.mgz : anatomical target
3. register-test.dat : O
Hi again
Yes, test.nii is the functional data registered to the anatomy.
The following files have now been uploaded to your filedrop and can be
downloaded by the email account "gr...@nmr.mgh.harvard.edu"
1. vol0001.nii.gz : functional input
2. orig.mgz : anatomical target
3. register-test.dat : O
And the functional is test.nii.gz? If so, can you upload
vol0001.nii.gz, register-test.dat, test.nii.gz, and orig.mgz to our file drop?
doug
On 04/25/2012 07:49 AM, Erlend Hodneland wrote:
> Both the fmri data registered to orig is mismatched, and also the original
> raw fmri data are mismatc
Both the fmri data registered to orig is mismatched, and also the
original raw fmri data are mismatched with orig,
see the link here showing our raw data (fmri, orig and 152MNI) shown in fslview
http://vedlegg.uib.no/?id=297a1242fa82b4b7565b470806254c5a
It is orig.nii converted from orig.mgz that
What images are mismatched? Specifically, which anatomical image are you
loading into fslview?
If you have not loaded the orig.mgz (converted to nii), then there will be be a
mismatch.
doug
On 04/24/2012 04:29 AM, Erlend Hodneland wrote:
> Hi again,
>
> We are trying to do the same as was done
Hi again,
We are trying to do the same as was done in Trachtenberg et al 2012
(Neurobiology of Aging), ie opt.the commonly used FLIRT+FNIRT
registration in FEAT with BBreg:
"For group analysis, functional data were registered, via the high
resolution anatomical image, to the Montreal Neurological
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
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 v
what do you mean 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.
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