Hello Doug,
sorry for the delay. But thank you for going through the log and giving me
helpful advice. The problems I was having with registration were down to the
fact that the anatomical (brain mask) and functional were oriented differently
and the flirt command line options (search angle in x
From the output it looks like the func-anat registration is off,
probably because of the partial FoV is causing the FSL registration used
to init BBR to be off (often happens with a partial FoV). Were the
anatomical and functional acquired at the same time? If so, then you'll
have to bypass r
The second warning you don't need to worry about. I should change that
to not be a warning. reg-feat2anat is only registering the functional
and anatomical. If the registration to mni152 does not look good, then
that is an FSL issue
doug
On 01/30/2014 11:06 AM, Mariam Sood wrote:
> Hello,
>
>
Hello,
I am running reg-feat2anat and facing some problems.
First I ran the command in its default mode using FSL initialisation
reg-feat2anat --feat featdir.feat --subject s. That gave me a bad registration.
There is a warning coming up
WARNING: initial G-W contrast is negative, but expec
That would be the same as specifying highres.nii.gz as the intermediate
registration (--int to bbregister). Is this what you tried?
doug
Cris Lanting wrote:
> Dear all,
> dear Doug,
>
>
>> If you have a partial FOV, then it
>> will probably fail. You can test this by running bbregister outsi
Which version of freesurfer are you running? At one point, reg-feat2anat
was dependent on the feat registration, but "now" it is not. I don't
know whether you fall into the "now" category. If you have a partial
FOV, then it will probably fail. You can test this by running
bbregister outside of
Dear all,
I'm having a slight problem with reg-feat2anat to transform functional
data (FSL) to anatomical (Freesurfer) in that the resulting
transformation seems completely wrong.
What I've done so far is the following:
1) run FEAT including the normal FEAT registration (which I know fails
due to
Hello,
I'm trying to display some FEAT statistics on a surface I created
using Freesurfer using instructions from
http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html. The automatic
registration function reg-feat2anat seems to have failed and I'm not
sure what I should do to re-orient the slices
