Hi Yolanda, that looks correct, though you might want to use mri_label2vol instead of mri_vol2vol. mri_label2vol will handle certain cases better (like when multiple conformed voxels land in a single rawavg voxel). But why do you need to go to rawavg space anyway? If you're going to just count voxels, it would be better to do it in the conformed space and not worry about what happens to the segmentation when you go do a lower res space.
doug Yolanda Vives wrote: > Thank you Bruce! > > I would like to segment a set of caudates into head and body and then > obtain the real volume of these two parts. The procedure that I am > applying is the following: > > 1.- Applying the standard recon-all process > 2.- Extracting the "conformed" voxel geometry caudate with > the following command: > > ./mri_extract_label $SUBJECTS_DIR/$subj/mri/aseg.mgz 11 > $PROJDIR/$subj.nii.gz > 3.- Segmenting the caudates into head and body > 4.- Transforming the head/body into the native sapece with the > following command: > > mri_vol2vol --mov Head_Left-Caudate.mgz --targ rawavg.mgz --regheader > --o Head_Left-Caudate-in-rawavg.mgz > 5.- Voxel counting > > Would it be correct? > > Thank you in advance, > Yolanda > > > > 2011/2/10 Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > > Hi Yolanda, > > the first command maps the aseg from the "conformed" voxel > geometry back to the voxel geometry on the scanner, and the second > extracts the caudate from that volume. If you want the caudate in > the conformed space, just use aseg.mgz in the mri_extract_label > command instead of aseg-in-rawavg.mgz > > cheers > Bruce > > > On Thu, 10 Feb 2011, Yolanda Vives wrote: > > Dear freesurfer's, > > I have run a conventional recon-all process and I am > interested in isolating > the caudate from my subjects. I have applied the following > commands: > > *./mri_label2vol --seg $SUBJECTS_DIR/$subj/mri/aseg.mgz --temp > $SUBJECTS_DIR/$subj/mri/rawavg.mgz --o > $SUBJECTS_DIR/$subj/mri/aseg-in-rawavg.mgz --regheader > $SUBJECTS_DIR/$subj/mri/aseg.mgz > * > *./mri_extract_label $SUBJECTS_DIR/$subj/mri/aseg-in-rawavg.mgz 11 > $PROJDIR/$subj.nii.gz > * > > I had seen in the wiki that these commands should be used when > we need the > images in native space. ¿Does it mean that my caudates are > "denormalized" or > on the contrary, that the images have only been resliced to > the original > size? If it is the second case, how could I obtain the > caudates from the > original image? > > Thank you for your help, > Yolanda > > > > 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. > > > > > -- > Yolanda Vives > PIC (Port d'Informació Científica) > Campus UAB, Edificio D > E-08193 Bellaterra, Barcelona > Telf. +34 93 586 8232 > http://www.pic.es <http://www.pic.es/> > Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > 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 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
