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
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