Gari

On Tue, Sep 25, 2012 at 5:57 PM, Douglas N Greve <greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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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