Hello All,
Thank you for the suggestions. I'll try makerot. tkregister2 looks quite promising altho I do not
have freesurfer installed on the computer where the data reside. If I get stuck with makerot, I'll
move my data over to where freesurfer is installed and try that next.
Thank you,
- BettyAnn
On Thu, 5 Jul 2007 14:58:28 -0400, Doug Greve <[log in to unmask]> wrote:
>If you have freesurfer installed, you can use tkregister2, something
>like:
>
>tkregister2 --targ $FSLDIR/etc/standard/avg152T1.img \
> --mov input-to-flirt.{nii,nii.gz,img} \
> --regheader --reg junk.reg --fslregout fsl.reg
>
>This will bring up an interface that you can use to examine and modify
>the registration. If you just want to use this to create fsl.reg, then
>you can run it non-interactively with --noedit. You can also give it
>an fsl matrix as input with --fsl fslinput.reg
>
>doug
>
>
>
>On Thu, 5 Jul 2007, Saad Jbabdi wrote:
>
>> Hi - you can use makerot to create a rotation matrix that you can feed to
>> flirt.
>>
>> saad
>>
>>
>> On 5 Jul 2007, at 19:12, Bettyann Chodkowski wrote:
>>
>>> Hello,
>>>
>>> Is there a utility to manually create a transformation matrix
>>> that could be used in flirt -init <matrix-filname>?
>>>
>>> For example, I have a dataset that would (probably) register
>>> to MNI-space better if only I could apply an initial rotation
>>> of 30deg about the z-axis. Vanilla registration results are
>>> poor due to disease.
>>>
>>> I could create a htm in matlab but I was unsure of handedness
>>> of your coordinate system and the how origin is handled. Also,
>>> what if I wanted to apply two rotations, the ordering, etc.
>>>
>>> If a utility already exists, that would relieve me from figuring
>>> all that out. Something like a reverse of avscale?
>>>
>>> Thank you,
>>> - BettyAnn
>>
>> ---------------------------------------------------------------------------
>> Saad Jbabdi,
>> Postdoctoral Research Assistant,
>> Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>> +44 (0) 1865 222545 (fax 222717)
>> [log in to unmask] http://www.fmrib.ox.ac.uk/~saad
>> ---------------------------------------------------------------------------
>>
>>
>>
>>
>>
>
>--
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>[log in to unmask]
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>In order to help us help you, please follow the steps in:
>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>===========================================================
==============
