Thanks for your help. When I tried to use Applyxfm to apply the matrix func2hires.mat to the
functional in order to registered it to the subject's structural, it creates a HUGE output file. Is
this supposed to happen?
I don't want to transform my data into standard space because all the subjects I'm working
with are tiny babies. I'd like to registered the subject's functional file (actually it's the
filtered_func_data.img file since I want the functional data to be motion corrected first) to the
hires structural to ensure the baby didn't move in between scans.
Many thanks again,
Jen
On Mon, 29 Sep 2003 22:46:10 +0100, Tim Behrens <[log in to unmask]> wrote:
>Hi there -
>
>The nearest file to what you want is called filtered_func_data.hdr in the
>.feat directory- This is the data after all the pre-stats have been
>applied (HP filtering/motion correction/slice-timimg correction/Grand-mean
>scaling). HOWEVER - these data have not been registered. Feat does all the
>first-level stats in functional space (for various reasons), and then, if
>standard space stats are required, the transform is applied to the stats
>outputs.
>
>If you want filtered_func_data in standard space then you will have to
>perform the registration stage - giving you a transform
>example_func2standard.mat in the reg directory.
>
>Then use the Applyxfm GUI (type Applyxfm), with filtered_func_data as the
>input, example_func2standard.mat as the transform and the standard image
>as the reference.
>
>Think this should give you what you want..
>
>Ta
>
>Tim
>
>-----------------------------------------------------------------------------
--
>Tim Behrens
>Centre for Functional MRI of the Brain
>The John Radcliffe Hospital
>Headley Way Oxford OX3 9DU
>Oxford University
>Work 01865 222782
>Mobile 07980 884537
>-----------------------------------------------------------------------------
--
>
>On Mon, 29 Sep 2003, Jennifer Townsend wrote:
>
>> In FEAT prestats, I only want to register my functional to structural
>> scan (and NOT the standard brain) and do motion correction. FSL creates
>> a number of files as a result and I'm not sure which to use. I want to
>> take my registered/motion corrected data in analyze format to use in
>> another program. Where would are these files located and how are they
>> named? the /mc folder doesn't have any analyze format image files and
>> the /reg only has "example_func".
>>
>> Many thanks for any help,
>> Jen
>>
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