Hi Doug, I am interested in coming back to rawavg space because we have the caudates segmented manually and we would like to compare the volumes obtained automatically with those obtained with a manual segmentation. In this case, is it necessary to come back to rawavg space, istn't it?
Yolanda 2011/2/11 Douglas N Greve <gr...@nmr.mgh.harvard.edu> > 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 > > -- Yolanda Vives PIC (Port d'Informació Científica) Campus UAB, Edificio D E-08193 Bellaterra, Barcelona Telf. +34 93 586 8232 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 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.
