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Subject:

Re: losing resolution with FLIRT

From:

"Christian F. Beckmann" <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 18 Oct 2004 20:44:09 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (77 lines)

Hi Heather

x-,y- and z-translations are stored in the last column of the matrix,
see
http://www.fmrib.ox.ac.uk/fslcourse/lectures/flirt_fugue/
s_3115matrix.htm for more details

hope this helps
cheers
christian



On 18 Oct 2004, at 20:35, Heather Emmerton wrote:

> Thank very much, the faq has been tremendously helpful.  I'm now
> having the
> problem that my centre of volume is not where it starting in my image.
> I see
> from the faq that I need to add an offset to the .mat transform file.
> Are the
> last four values (the bottom row - 0 0 0 1) of this file offsets? I
> wasn't
> really clear on which values to change to add the offset.
> Thanks again!!
> Heather
>
> ----- Original Message -----
> From: "Christian F. Beckmann" <[log in to unmask]>
> Date: Monday, October 4, 2004 3:48 pm
> Subject: Re: [FSL] losing resolution with FLIRT
>
>> Hi Heather,
>>
>> it's in the FAQ, have a look at
>> http://www.fmrib.ox.ac.uk/fslfaq/#flirt_resample
>> cheers
>> christian
>>
>>
>> On 4 Oct 2004, at 23:43, Heather Emmerton wrote:
>>
>>> Hello,
>>> I intend to use FLIRT to register images to the MNI avg152T1
>> standard> brain.
>>> Seems to be working well, as the alignments are coming out nicely,
>>> however
>>> since FLIRT uses the reference image format in the output I
> am
>> losing> resolution in my image as my images are being shrunk from
>> 256x256x124> to
>>> 91x109x91 pixels. Is there any way to stretch the MNI image into my
>>> coordinate space before running FLIRT, so my output images are
>> the same
>>> size as my input images?
>>> Thanks for your help!
>>> Heather
>>>
>> --
>>  Christian F. Beckmann
>>  Oxford University Centre for Functional
>>  Magnetic Resonance Imaging of the Brain,
>>  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>>  Email: [log in to unmask] -
>> http://www.fmrib.ox.ac.uk/~beckmann/  Phone: +44(0)1865 222782 Fax:
>> +44(0)1865 222717
>>
>
>
--
  Christian F. Beckmann
  Oxford University Centre for Functional
  Magnetic Resonance Imaging of the Brain,
  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
  Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
  Phone: +44(0)1865 222782 Fax: +44(0)1865 222717

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