Ok, I see. Thank you. Just one more question. MRIs from my "manually segmented" caudates have been previously reoriented according to the Anterior/Posterior Commissure axis. Are freesurfer segmented images reoriented also in this way?
Cheers, Yolanda 2011/2/14 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > not if you just want to compare volumes. If you want to compute overlap it > would be, but note that you'll probably be biased towards lower overlap as > you will induce some sampling errors mapping the aseg to the original voxel > space. > > cheers > Bruce > > > > On Mon, 14 Feb 2011, Yolanda Vives wrote: > > 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
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