I have both. In origin, the ROI-s are 2mm volume based .nii that I
convert to FS .mgh with register.dat I obtained with bbregister.
-- In the case of label2label method I create the surface version
with mri_vol2surf (and the correspondence is perfect), and then use
mri_label2label in order to get the CT averages.
-- In the case of surf2surf, I use the volume based .mgh with
mri_preproc (mri_surf2surf)
thanks!
Gari
On Tue, Sep 25, 2012 at 5:57 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu>> wrote:
So you have ROIs in Colin27 space and you want to map them into
your CT space and compute average CT intensities over them? Are
the ROIs volume-based or surface-based?
doug
On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote:
Hi Doug,
many thanks for your answer, I try to detail it more:
1.- bbregister is registering two Colin27 brains. First one is
a 2mm found in spm/canonical/single_subject_T1.nii, and second
one is the FS_spm_Canonical found in SurfRend distribution. It
was in .COR format and I run recon-all to have a modern
version of it. As they are almost the same brain the
registration matrix is quite simple and the registration was
perfect. This way I had exactly the same ROI-s for Colin27 in
SPM and in FS (it did not work that well for fsaverage, that's
why I took this approach).
2.- In any case, I have several ROI-s in Colin27 space in FS,
and then when I try to obtain average CT values from my
subjects I use these 2 different approaches: label2label and
surf2surf.
mri_anatomical_stats is run on the labels created by
mri_label2label.
If you think it will be of help I can send the detailed
command line calls,
thanks!
Gari
On Sat, Sep 22, 2012 at 12:47 AM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu>
<mailto:gr...@nmr.mgh.harvard.edu
<mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
Hi Gari, I'll need more information. I can't tell what you
are doing.
Eg, what is being registered with BBR? what is
mris_anatomical_stats run
on? Where does Colin27 come into it and why?
doug
On 09/19/2012 06:15 PM, Garikoitz Lerma-Usabiaga (Gari) wrote:
Dear Freesurfers,
We've been comparing 2 different methods to obtain CT averages
for 4 Volume ROI-s (volume ROI-s were in Colin27 space).
We've used the 40 buckner subjects for the comparisons.
METHOD L2L: bbregister>> mri_vol2surf (mgh)>>
mri_binarize (mgh)>> mri_cor2label (label)>>
mri_label2label>>
mris_anatomical_stats
METHOD S2S: bbregister>> mri_vol2surf>> mri_preproc
(mri_surf2surf)>> mri_segstats
After performing t-test-s over the results, we can observe that
the results are in many cases different.
-- Is there a way to choose the "best" method? Which one should
we use for our work and why?
Many thanks again for your help,
Gari
PD We've tabulated a third method as well:
METHOD SurfRend: Surfrend (.w)>> mri_surf2surf(.mgh)>>
mri_binarize(.mgh)>> mri_cor2label (.label)>>
mris_anatomical_stats
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