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Hi

On 3 Jul 2013, at 17:57, Qasim Bukhari <[log in to unmask]> wrote:

Hi
Thanks for the reply. 
I understand it for a model based GLM analysis, but if I m using a seed-voxel in my GLM, I anyway have to do the registration of the mask with the individual subject data in order to define the seed. Right ? So that means we anyway have to do one registration step of registering the mask with all the individual subjects. In that case dont you think it is better to do the complete registration prior to using GLM.

Again, you can do it either way.  One easy way to get a standard-space mask into the native FMRI space (if that's the way you want to do it) is to use it as a mask in Featquery, which will leave a native-space version of the mask in its output folder.

Cheers.


Or is there any other approach as well that I can use to avoid the registration before GLM even in this case ? Because if I understood correctly the reason you mentioned, then I would always prefer doing registration after GLM.

Thanks again
best regards,
Qasim

Qasim Bukhari
Research Assistant and Doctoral Candidate
Institute for Biomedical Engineering
ETH and University Zurich
Wolfgang-Pauli-Strasse 27, HIT E22
webpages: MR-page




Date: Wed, 3 Jul 2013 16:53:13 +0100
From: [log in to unmask]
Subject: Re: [FSL] registration or GLM first
To: [log in to unmask]

Hi - both strategies are in theory fine - the original reason we did the GLM first in FSL was for practical purposes (to save having to do the GLM with autocorrelation modelling on higher resolution resampled data).
Cheers.




On 3 Jul 2013, at 15:14, Qasim Bukhari <[log in to unmask]> wrote:

Please can somebody reply me to understand the processing pipelines
I have been told that it is possible to do the between-subject registration after doing GLM and actually this is the way how FSL works internally. I had been using SPM in the past and I was always of the view that one must do the registration before GLM since I always included registration in the pre processing. In SPM one doesnt have any other choice of doing registration later as I mentioned above.
Can someone please explain if both strategies are ok, and what is the actual difference if we do the registration after GLM ?

Thanks a lot

Qasim Bukhari
Research Assistant and Doctoral Candidate
Institute for Biomedical Engineering
ETH and University Zurich
Wolfgang-Pauli-Strasse 27, HIT E22
webpages: MR-page




Date: Tue, 2 Jul 2013 21:15:35 +0000
From: [log in to unmask]
Subject: [FSL] registration or GLM first
To: [log in to unmask]

Dear all,
I have a confusion; is it ok to first take all the subjects in to native space; and do the GLM and then do the registration ?? 

Thanks a lot
and best regards

Qasim Bukhari
Research Assistant and Doctoral Candidate
Institute for Biomedical Engineering
ETH and University Zurich
Wolfgang-Pauli-Strasse 27, HIT E22
webpages: MR-page





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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
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Stop the cultural destruction of Tibet







---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
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Stop the cultural destruction of Tibet