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Hi Paul,


Thank you a lot for your answer.

Not, I only selected FLIRT with 12 DOF....this is why I was trying to run non-linear registration (FNIRT) and then Applywarp but it is not working. I thing I did a mistake is that I should not have tryied to run FLIRT again....

But I only have example_fun2standard.mat....so having only affine matrix...how should to conduct?

Maybe:

fnirt --ref=.../.../MNI152_T1_2mm_brain.nii.gz --in=rendered_thresh_zstat1 --aff=example_fun2standard.mat --config=T1_2_MNI152_2mm.cnf --cout=fmri_to_MNI_field --iout=rendered_thresh_zstat1_fnirted

applywarp --ref=../.../MNI152_T1_2mm_brain --in= rendered_thresh_zstat1.nii.gz --warp= --out=fmri_to_MNI_field --out=warped_rendered_thresh_zstat1

Is that right now?

Kind regards,

Rosalia


2016-11-21 15:05 GMT+01:00 paul mccarthy <[log in to unmask]>:
Hi Rosalia 

(see my last email regarding the rendered_thresh files).

Did you select non-linear registration when you set up Feat? If so, you should have a file 'reg/example_func2standard_warp.nii.gz'. 

Pass this file to the 'applywarp' command to transform from the subject functional space to MNI152 space. For  example:

applywarp -i thresh_zstat1 -r $FSLDIR/data/standard/MNI152_T1_2mm -o thresh_zstat1_standard -w reg/example_func2standard_warp

Cheers,

Paul

On 20 November 2016 at 21:43, Rosalia Dacosta Aguayo <[log in to unmask]> wrote:
Dear FSL experts,

I have finally solved the problem regarding seeing the activations...just was a problem with setting min and max values.

The problem now is that I am trying to make a non linear registration with fnirt setting the following:

fnirt --ref=MNI152_T1_2mm_brain.nii.gz --in=rendered_thresh_zstat1.nii.gz -aff=example_func2standard.mat --iout= rendered_thresh_zstat1_fnirted

But it seems that there is something that does not work....

Any one of you could help me with this problem?

Kind regards,

Rosalia