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Thank you Mark.
That worked.
My other scripts on separate dataset were working fine, only this
particular script had a glitch.
Thanks for your help.
Suril

On Fri, Sep 7, 2012 at 1:23 AM, Mark Jenkinson <[log in to unmask]> wrote:

> Dear Suril,
>
> I think you have a problem in that you creat func2struct_RESTEC1.mat twice
> (both of the two flirt calls at the start use the same output name) so this
> file is not the func2struct registration, but actually the struct2standard.
>  In the fnirt call this is fine (as you should be using the struct2standard
> affine here).  But in the final applywarp call the --premat really does
> need to be the func2struct, which you don't have at that point.
>
> If you change the names for the affine matrices in steps 1 and 5 (first
> flirt call and second applywarp call) then I think this should work.
>
> All the best,
> Mark
>
>
> On 6 Sep 2012, at 19:42, SURIL GOHEL <[log in to unmask]> wrote:
>
>
> Hi FSL experts,
>
> I am facing troubles with FNIRT registration of my functional data using
> anatomical.
>
> I am using following command lines.
>
>
> `flirt -ref mprage_betted.nii.gz -in fin_RESTEC1_1tp.nii.gz -dof 7 -omat
> func2struct_RESTEC1.mat`;
>
> `flirt -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -in
> mprage_betted.nii.gz -omat func2struct_RESTEC1.mat`;
>
> `fnirt --in=MPRAGE.nii.gz --aff=func2struct_RESTEC1.mat
> --cout=struct2standard_fnirt_RESTEC1 --config=T1_2_MNI152_2mm`;
>
> `applywarp --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm
> --in=MPRAGE.nii.gz --warp=struct2standard_fnirt_RESTEC1
> --out=reor_MPRAGE_fnirt`;
>
>
> `applywarp --ref=MNI152_T1_2mm.nii.gz --in=fin_RESTEC1_1tp.nii.gz
> --warp=struct2standard_fnirt_RESTEC1 --premat=func2struct_RESTEC1.mat
> --out=fin_RESTEC1_1tp_mni3_fnirt`;
>
>
> The problem is anatomical file is fine after registration and matches well
> with 2mm MNI brain but my functional scan is not registered.
> The functional brain is shifted to the right and only half of the scan is
> registered.
>
> All my data is in RPI orientation.
>
> The only problem i can think of is that my functional scans are sagittal
> scans while my anatomical scans are axial scans.
>
> Attached are the AFNI screen shots of registered images.
> Any help would be greatly appreciated.
>
> --
> -Suril
> 973-972-7076
>
>
>
> <anatomy.png><functional.png>
>
>
>