I would guess that if the input highres brain is the same, then the
highres2tandard and its inverse should be the same in the three folders
(unlike the example_func2highres and example_func2standard).
So it should probably ok if you use the matrix from one of the 1stlevels
(but this is where I should make clear that I'm a USER, so Mark may
disagree).
Of course, if you'd rather play it safe and use the matrix from each
1stlevel, all you have to do is to change, in the flirt command, the
1stlevel folder you get the standard2highres matrix from:
-init 1stlevel_A.feat/reg/standard2highres.mat
-init 1stlevel_B.feat/reg/standard2highres.mat
-init 1stlevel_C.feat/reg/standard2highres.mat
all the rest of the command is identical for all three.
cheers
martin
Virve Vuontela wrote:
> Hi,
> thank you for the quick reply, but since I have 3 first-level analyses and
> therefore 3
> separate reg/standard2highres.mat -files for this subject, I'm still
> wondering whether it
> is OK to use any of those files with registration information. Somehow I
> thought that
> these 3 standard2highres.mat -files are not identical, but contain at least
> small
> differences. Can I assume that the differences are small enough to be
> ignored and will
> not affect the results?
>
> Virve
>
>
> Date: Tue, 26 May 2009 10:37:05 +0100 [12:37:05 PM EEST]
> From: "Martin M Monti" <[log in to unmask]>Add
> [log in to unmask] to my
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> To: [log in to unmask] [log in to unmask] to my Address Book
> Reply-To: "FSL - FMRIB's Software Library" <[log in to unmask]>Add
> [log in to unmask]
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> Subject: Re: [FSL] Higher-level analysis for one subject
> Vivre,
>
> the file you are looking for is in the first level analysis folders: e.g.
> 1stlevel.feat/reg/standard2highres.mat
>
> type 'flirt' in your terminal window, the third example is probably what you
> want to use.
>
> Something like:
> flirt -in highlevel.gfeat/thresh_zstat1 -ref highres_image -out
> thresh_zstat1_2_highres
> -init 1stlevel.gfeat/reg/standard2highres.mat -applyxfm
> cheers
>
> martin
>
> Virve Vuontela wrote:
>
> [Hide Quoted Text]
> Dear FSL community,
> I have run first-level FEAT analyses for one subjects's three fMRI runs and
> after that followed the instructions in your FAQ page to combine these runs
> in a higher-level FEAT analysis and this worked fine so far. But now I need
> to put the results of the higher-level analysis on the subject's own high
> resolution brain. How to accomplish this? It seems that all copes in the
> gfeat-folder are already in the standard space and there is only one
> mat-file which probably does not include information of the registration
> part of the analysis...? Thank you for your help in advance!
>
> Virve Vuontela
>
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