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
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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