Rachel:
Check out this setting in spm_defaults.
% Create What? Give flexibility about which images are written resliced,
% or remove an extra question.
%-----------------------------------------------------------------------
%sptl_CrtWht = 1; % All Images + Mean Image
sptl_CrtWht = -1; % Full options
If the % sign is in front of the second option and not the first then
you're right all images + the mean image will be created with
reslicing. Your choices are
1) see if you can get the spm_defaults.m file changed at your site.
2) if not put a copy of spm_defaults in your home directory and make
sure it is listed higher on the matlab path than spm. That way spm
will use the files in your home directory first.
Darren
At 1:06 PM -0500 9/25/2000, Rachael Seidler wrote:
>Thanks Darren, Stephen for the suggestions..
>I have a question about one of the steps you suggested, tho:
>>1) realign functionals to some common functional image if possible.
>>Write out a
>>mean image but don't reslice functionals at this point.
>Under the realign options, if I choose coregister and reslice then
>all of the functionals are resliced. If I choose coregister only,
>then I don't get the option to write the mean image. Is there a way
>to write the mean image without reslicing all of the functionals?
>Thanks again,
>Rachael
>Rachael D. Seidler, PhD
>University of Minnesota Dept of Neuroscience
>and Brain Sciences Center, 11B
>Veterans Affairs Medical Center
>One Veterans Drive
>Minneapolis, MN 55417
>Phone: 612 725-2000 x.1765
>Fax: 612 725-2291
>Email: [log in to unmask]
>
>
>>2) coregister T1 to the mean functional image. Don't write out a
>>new T1 image at
>>this point.
>>3) Normalize the T1.
>>4) apply the normalization parameters from the T1 to your functional volumes-
>>this will reslice the functionals. (make sure you set the
>>normalization defaults
>>to allow you to choose the voxel size of the functional images).
>>
>>You should now have normalized T1 and functional images. Assuming
>>good quality
>>T1 images from subjects with reasonably normal brains, and good
>>coregistration
>>between T1 and functionals you should have minimal distortions (or
>>no more than
>>were there originally).
>>
>>HTH,
>>Darren
>>
>>Rachael Seidler wrote:
>>
>> > Hello all,
>> > I'm having a problem normalizing some mri functional images that contain
>> > distortions. Specifically, there is no visible data in the inf. frontal
>> > region of these images.. When I normalize them to the epi
>>template however,
>> > everything gets stretched forward to fill in the empty space. I suspect
>> > this distorts the signal outside of the original distortion region. Is
>> > there a way to normalize anatomical images to the standardized space, and
>> > then apply these parameters to the functional data? Or can
>>anyone recommend
>> > another fix?
>> > Thanks in advance,
>> > Rachael
>> > Rachael D. Seidler, PhD
>> > University of Minnesota Dept of Neuroscience
>> > and Brain Sciences Center, 11B
>> > Veterans Affairs Medical Center
>> > One Veterans Drive
>> > Minneapolis, MN 55417
>> > Phone: 612 725-2000 x.1765
>> > Fax: 612 725-2291
>> > Email: [log in to unmask]
>> > _________________________________________________________________________
>> > Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com.
>> >
>> > Share information about yourself, create your own public profile at
>> > http://profiles.msn.com.
>>
>>--
>>----------------------------------------------------------------------
>>Darren R. Gitelman, M.D. E-mail: [log in to unmask]
>>Cognitive Neurology and Voice: (312) 908-9023
>> the Alzheimer's Disease Center Fax: (312) 908-8789
>>http://www.brain.nwu.edu
>>Northwestern Univ., 320 E. Superior St., Searle 11-470, Chicago, IL 60611
>>----------------------------------------------------------------------
>>
>>
>
>_________________________________________________________________________
>Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com.
>
>Share information about yourself, create your own public profile at
>http://profiles.msn.com.
-------------------------------------------------------------------------
Darren R. Gitelman, M.D.
Cognitive Neurology and Alzheimer's Disease Center
E-mail: [log in to unmask] WWW:
http://www.brain.northwestern.edu
Voice: (312) 908-9023 Fax: (312) 908-8789
Northwestern Univ., 320 E. Superior St., Searle 11-470, Chicago, IL 60611
-------------------------------------------------------------------------
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|