OK, got it (finally). I would not expect the answers to be identical, but I would expect them to be "close".  How close are they? If the ROI is very small, there might be appreciable differences between the two.

doug


On 9/27/12 6:26 PM, Garikoitz Lerma-Usabiaga wrote:
Hi,
You are right, this was one of the methods. The second one is as follows (I copy the repeated steps):

For a given ROI, you have a nifti file (roi.nii) in 2mm space defined on colin27. This ROI volume has a voxel value == 1 if it is in the ROI or 0 if it is out.

You have a registration between roi.nii and orig.mgz

You run mri_vol2surf on roi.nii to get lh.roi.mgh

I run mris_preproc for every subject to Colin27: mris_preproc --out /subject/surf/ROI_toColin27.mgh --target Colin27 --hemi lh --meas thickness --s subject

mri_segstats --seg /Colin27/surf/lh.roi.mgh --in /subject/surf/ROI_to_Colin127.mgh --sum subject/stats/target_lh.ROI.stats


Thanks for your help, 
Gari


Note:
You said: You run mri_cor2label (with --surf option) to convert lh.roi.mgh into lh.roi.label
Just in case, this is how I run it:



On 26/09/2012, at 23:56, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Sorry, I'm still a little lost. Let me see if I have it right:

For a given ROI, you have a nifti file (roi.nii) in 2mm space defined on colin27. This ROI volume has a voxel value == 1 if it is in the ROI or 0 if it is out.

You have a registration between roi.nii and orig.mgz

You run mri_vol2surf on roi.nii to get lh.roi.mgh

You run mri_cor2label (with --surf option) to convert lh.roi.mgh into lh.roi.label

You run mri_label2label on lh.roi.label to map it into an individual subject

You run mris_anatomical_stats on the individual lh.roi.label file

Does this describe one of your processing streams correctly? If so, what is the other processing stream (given in this kind of detail)?

doug



On 09/25/2012 04:43 PM, Garikoitz Lerma-Usabiaga wrote:
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 <greve@nmr.mgh.harvard.edu <mailto: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>
      <mailto: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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