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