Begin forwarded message:

*From:* Garikoitz Lerma Usabiaga garikoitz@gmail.com *To:* Louis Nicholas Vinke vinke@nmr.mgh.harvard.edu *Subject:* *Re: [Freesurfer] Register ROI5.nii to fsaverage in tutorial "Cortical Thickness of a Volume-defined ROI"?*

Thanks for your answer Louis,

I think I'm using it, the steps were: 1- Correct visualization of ROI with: tkmedit -f TT_avg152T1.nii -overlay ROI45.nii -fthresh 0.5

2- I execute spmregister: spmregister --s fsaverage --mov ../../ROI2/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat

3.-Incorrect visualization when I execute: tkmedit fsaverage T1.mgz -overlay ../../ROI2/ROI45.nii -overlay-reg TT_avg152T1_to_fsaverage.dat -fthresh 0.5 -surface lh.white -aux-surface rh.white

What I understand is that the .dat is a transformation matrix between TT_avg152T1 and fsaverage, so when I am asking to overlay ROI45.nii, I am asking tkmedit to transform it to fsaverage by the .dat file. Is that correct? What do you think that could be the error? I am attaching the images just in case...

Thanks again, Gari

PS This is the TT_avg152T1_to_fsaverage.dat: fsaverage 2.000000 2.000000 0.150000 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0 0 0 1 round

On 2012-07-12, at 17:56, Louis Nicholas Vinke wrote:

Hi Gari,

When you view the ROI5.nii on fsaverage make sure you include

'-overlay-reg TT_avg152T1_to_fsaverage.dat'. TT_avg152T1_to_fsaverage.dat is the transformation computed in the previous step which you need to apply. Nothing was resampled in step 2.

-Louis

On Thu, 12 Jul 2012, Garikoitz Lerma Usabiaga wrote:

Dear All, I am trying to automate ROI creation in freesurfer following

the VolumeRoiCorticalThickness tutorial, based on the AAL defined ROI-s from MarsBar.

QUESTION

ROI5.nii was originally in the same space as TT_avg152T1.nii (see MORE INFO below).

I understand that after Step 2 (when TT_avg152T1.nii is registered to fsaverage with

spmregister), TT_avg152T1 will be in fsaverage space.

But, we didn't transform or register ROI5.nii, so I understand that it will continue in the same

original space.

When I visualize ROI5 over the original TT_avg152T1 it is ok, but when I visualize it over the

fsaveraged one, it is not.

Shouldn't we need to register or normalize ROI5.nii to fsaverage as well prior to the

mri_vol2surface mapping?

MORE INFO:

1.- I created the ROI5.nii in MarsBar: "ROI definition" > "Export" > "Export ROI to image"

(select: MNI_Frontal_Inf_Tri_L_roi.mat) > from image (select: avg152T1.nii)

Save it (name:

ROI45.nii)

2.- I follow exactly the same steps as the tutorial, but in step 3) when I check the ROI in the

inflated surface, it is clearly out of place...

Thank you very much in advance,

Gari

Garikoitz Lerma Usabiaga

Predoctoral Researcher

www.bcbl.eu

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