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 > <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>>> 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> > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel: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> > 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> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 <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> > > -- 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
