Dear Sue,
You can upload your original image and registered result to:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgiand send me the reference number.
I'm not sure that I will agree that it "looks like a brain" though,
as a normal brain image does not have identifiable brodmann
areas given by numbers! Is there an image that this is already
registered with that which is more like a brain? If you did have
something like this then also send it to the upload above.
All the best,
Mark
On 23 Feb 2011, at 17:51, Sudhin A. Shah wrote:
> Hi, Yes it looks like a brain, with ~37 different areas, all with a unique number. i.e. Area 1 has voxel values of 1 etc.. When I extract a seed from the original template, I can get just one chunk of like valued voxels. After registration to MNI space, it still looks like a brain, but the boundaries are all weird. When I then try to extract an area, I get a weird chunk and tiny voxels outside the area (almost like an outline of the brain). Is there an email address I can send attachments to? I could send you the template and seeds..
>
> Thanks,
> S
>
> On 02/23/11, Mark Jenkinson <
[log in to unmask]> wrote:
>> Dear Sue,
>>
>> I don't know this image - does it look like a brain or is it an
>> image with just constant label values in it (a collection of
>> ROIs)? If it is the latter then you cannot expect it to register.
>> You can only register two things together than contain
>> similar information (i.e. tissue boundaries, etc.)
>>
>> If it does look like a brain then it should be possible to
>> register and you'll need to give me more information about
>> in what ways it is failing. I couldn't understand your sentence
>> about blurry seeds.
>>
>> The option -odt short is for fslmaths, not flirt, so I think
>> you are getting confused there.
>>
>> All the best,
>> Mark
>>
>>
>>
>> On 23 Feb 2011, at 17:14, Sudhin A. Shah wrote:
>>
>> > Hello,
>> >
>> > I have a problem using flirt to register a template (brodmann.nii.gz from MRICRON) to MNI space.
>> >
>> > This is the command I used:
>> > flirt –in brodmann.nii.gz \
>> >
>> > –ref $FSLDIR/data/standard/MNI152_T1_2mm_brain \
>> >
>> > –out brodmann.reg2mni \
>> >
>> > –omat brodmann.reg2mni.mat \
>> >
>> > –bins 256 –cost corratio \
>> >
>> > –searchrx -90 90 \
>> >
>> > –searchry -90 90 \
>> >
>> > –searchrz -90 90 \
>> >
>> > –dof 12 \
>> >
>> > –interp trilinear
>> >
>> >
>> > Seeds generated with the second file are blurry and contain voxels outside the target areas.
>> >
>> >
>> > I tried adding -odt short to the command line but got an error Unrecognised option. I am using FSL in Ubuntu/Linux.
>> >
>> >
>> > Can you please help/
>> >
>> >
>> > Thanks,
>> >
>> > Sue
>> >
>> >
>> >
>
> --