Register ROI5.nii to fsaverage in tutorial "Cortical Thickness of a Volume-defined ROI"?
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
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
freesurfer@nmr.mgh.harvard.edu
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Garikoitz Lerma Usabiaga -
Louis Nicholas Vinke