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
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
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
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.
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 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
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, YolandaThe 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 greve@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
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, YolandaThe 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 greve@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
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, YolandaThe 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 greve@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
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, YolandaThe 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 greve@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
yes, it is.
doug
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 mailto: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> <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 http://www.pic.es <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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
But "aseg.mgz" file comes from a Talairach-registered image and the anterior and posterior commissures are the standard alignment of the brain for this atlas. Could I assume that all my caudates come from MRIs that had the same orientation according to the anterior and posterior commissures?
yolanda
2011/2/14 Douglas N Greve greve@nmr.mgh.harvard.edu
yes, it is.
doug
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 mailto: 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> <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 http://www.pic.es <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
The aseg.mgz is in the subject's native anatomy (no stretching or compressing). As Bruce says, if you're just computing volumes, you don't need to do the transformation. If you want to compute overlap, then you need them in the same voxel-for-voxel space.
doug
Yolanda Vives wrote:
But "aseg.mgz" file comes from a Talairach-registered image and the anterior and posterior commissures are the standard alignment of the brain for this atlas. Could I assume that all my caudates come from MRIs that had the same orientation according to the anterior and posterior commissures?
yolanda
2011/2/14 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
yes, it is. doug 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 <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto: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> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> <mailto: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 http://www.pic.es <http://www.pic.es/> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://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 <http://www.pic.es/> Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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 http://www.pic.es/ Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Yolanda Vives