Re: [Freesurfer] Segmentation into native space

no, we don't reorient to avoid additional blurring cheers Bruce

On Mon, 14 Feb 2011, Yolanda Vives wrote:

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 fischl@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 greve@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 <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

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