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
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
