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 <
fischl@nmr.mgh.harvard.edu
<mailto:
fischl@nmr.mgh.harvard.edu>
<mailto:
fischl@nmr.mgh.harvard.edu
<mailto:
fischl@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