the latter option worked like a charm -- thanks!
koene
On Thu, 3 May 2012 06:07:49 +1000, Mark Jenkinson <[log in to unmask]> wrote:
>Hi,
>
>You can either pick an axis that represents these rotations all together
>and adjust the angle appropriately - e.g. axis of (-30,2,2) but normalised
>to unit length and an angle of sqrt(30^2+2^2+2^2). Alternatively, generate
>three separate rotations and combine them using convert_xfm with
>the -concat option.
>
>In general, combining rotations is tricky as the order is important, but
>it probably won't make too much difference for this example.
>
>All the best,
> Mark
>
>
>On 3 May 2012, at 06:03, Koene Van Dijk wrote:
>
>> thanks Mark, that's another cool tool.
>>
>> I ran the following but it's just short of what would be perfect:
>> makerot -c 80,80,47 -a 1,0,0 --theta=-30 -o matrix.mat
>>
>> After applying that matrix using flirt it's doing almost what I want: namely the output image was rotated 30 degrees around the x-axis.
>>
>> Now I would like to fine-tune:
>> rotate around x: -30 degrees (what I did)
>> rotate around y: 2 degrees
>> rotate around z: 2 degrees
>>
>> Is it easy to say how I can accomplish that in one transformation matrix?
>>
>> Thanks,
>> Koene
>>
>> =========================
>> Usage:
>> makerot [options] --theta=angle
>>
>> Compulsory arguments (You MUST set one or more of):
>> -t,--theta angle of rotation (in degrees)
>>
>> Optional arguments (You may optionally specify one or more of):
>> -a,--axis <ax,ay,az> unnormalised axis vector (comma separated)
>> --cov image filename used for centre of volume
>> -c,--centre <cx,cy,cz> centre of rotation in mm (comma separated)
>> -o,--out output filename for matrix
>> -v,--verbose switch on diagnostic messages
>> -h,--help display this message
>> =========================
>>
>>
>>
>>
>>
>>
>> On Thu, 3 May 2012 05:28:31 +1000, Mark Jenkinson <[log in to unmask]> wrote:
>>
>>> Yes - use "makerot" to generate a FLIRT transformation.
>>>
>>> All the best,
>>> Mark
>>>
>>> On 3 May 2012, at 05:26, Koene Van Dijk wrote:
>>>
>>>> Hi there,
>>>> I'd like to rotate an image just a little bit: e.g. just 30 degrees around the x-axis. Is there a nice fsl tool/command for that?
>>>>
>>>> I've been using fslswapdim for 90 or 180 degree swaps but this is different. I looked into using flirt, e.g.:
>>>> flirt -in input.nii.gz -ref copy_of_input.nii.gz -out output.nii.gz -applyxfm -init matrix.mat
>>>>
>>>> ... but I don't know what to use as matrix.mat. I've read in old posts that rotation and translation (with a normal flirt output.mat when registering one image to another) are highly related and it seemed much to complex for what I want: just a rotation and no translation and the center of the image may remain what it is now: 80 80 47 (so my input image has these dimensions: 160 x 160 x 94).
>>>>
>>>> Thanks for any help,
>>>> Koene Van Dijk
>>>>
>>
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