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.eduwrote:
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.**edugreve@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 > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve@nmr.mgh.harvard.edu>Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
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