Hi, I am calculating hippocampus volumes with 5.2 in CentOS 4.
I compare volumes (the same apply for lh and for rh) when calculating as:
Left.Hippocampus value in 1mm3 from aseg.stats I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and
obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in order to get mm3, and sum every column except left_hippocampal_fissure.
I obtain quite different values, for example: row.names lh.aseg lhHIP rh.aseg rhHIP 1S_00 4848.83828.187 4878.83767.7392 S_02 4153.83371.517 4547.63389.918 Am I doing anything wrong? Should I calculate the hippos subfields volumes differently?
Many thanks! Gari
Dear Gari, The subfield module uses a different, independent method to segment the hippocampus, and consistency with ASEG results is not explicitly enforced. That said, the subfield module is inialialized with the ASEG, and the results should be pretty close to each other, for the most part. Have you visually inspected the segmentation for those cases in which the difference looks large? Thanks, /Eugenio
On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote:
Hi, I am calculating hippocampus volumes with 5.2 in CentOS 4.
I compare volumes (the same apply for lh and for rh) when calculating as:
Left.Hippocampus value in 1mm3 from aseg.stats I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and
obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in order to get mm3, and sum every column except left_hippocampal_fissure.
I obtain quite different values, for example:
row.names lh.aseg lhHIP rh.aseg rhHIP 1 S_00 4848.8 3828.187 4878.8 3767.739 2 S_02 4153.8 3371.517 4547.6 3389.918
Am I doing anything wrong? Should I calculate the hippos subfields volumes differently?
Many thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Juan Eugenio, we have visually inspected the segmentations, and we observe that the volume differences between aseg and hippo-subfields are constants among subjects, and consistent in both left and right hemispheres (please see table attached, columns diff.aseg.left.subfields and diff.aseg.right.subfields). Indeed, the percentage of the difference between the aseg and the hippo-subfields is about 20% average (19.5% for the left and 22.1% for the right hemisphere), and there are not strong differences at the individual subject level.
The aseg values always are bigger than the hippo-subfields across all planes (please see attached photos with some examples). And, as it can be seen in the attached pictures, the hippo-subfield segmentation seems to be more accurate than the aseg one.
We used the standard recon-all procedure with -hippo-subfields -qcache -all
Considering that these differences are pretty consistent across subjects, Do you think that there is anything wrong with our results? Or anything that we are missing in our analysis?
Thank you very much, Gari
[image: Inline image 1]
On Mon, Feb 25, 2013 at 5:09 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote:
Dear Gari, The subfield module uses a different, independent method to segment the hippocampus, and consistency with ASEG results is not explicitly enforced. That said, the subfield module is inialialized with the ASEG, and the results should be pretty close to each other, for the most part. Have you visually inspected the segmentation for those cases in which the difference looks large? Thanks, /Eugenio
On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote:
Hi, I am calculating hippocampus volumes with 5.2 in CentOS 4.
I compare volumes (the same apply for lh and for rh) when calculating as:
Left.Hippocampus value in 1mm3 from aseg.stats I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and
obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in order to get mm3, and sum every column except left_hippocampal_fissure.
I obtain quite different values, for example:
row.names lh.aseg lhHIP rh.aseg rhHIP 1 S_00 4848.8 3828.187 4878.8 3767.739 2 S_02 4153.8 3371.517 4547.6 3389.918
Am I doing anything wrong? Should I calculate the hippos subfields volumes differently?
Many thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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.
I have noticed that Freesurfer tends to include white matter in superior hippocampus (e.g. alveus), perhaps this is not included in the hipposubfields volumes?
Wondering, if I were to take a hand traced hippocampus rename it to aseg.mgz, and made sure that the label matched what Freesurfer expects, would the hipposubfields algorithm do its magic on this volume? Joshua
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Tue, Feb 26, 2013 at 9:48 AM, Garikoitz Lerma-Usabiaga < garikoitz@gmail.com> wrote:
Thanks Juan Eugenio, we have visually inspected the segmentations, and we observe that the volume differences between aseg and hippo-subfields are constants among subjects, and consistent in both left and right hemispheres (please see table attached, columns diff.aseg.left.subfields and diff.aseg.right.subfields). Indeed, the percentage of the difference between the aseg and the hippo-subfields is about 20% average (19.5% for the left and 22.1% for the right hemisphere), and there are not strong differences at the individual subject level.
The aseg values always are bigger than the hippo-subfields across all planes (please see attached photos with some examples). And, as it can be seen in the attached pictures, the hippo-subfield segmentation seems to be more accurate than the aseg one.
We used the standard recon-all procedure with -hippo-subfields -qcache -all
Considering that these differences are pretty consistent across subjects, Do you think that there is anything wrong with our results? Or anything that we are missing in our analysis?
Thank you very much, Gari
[image: Inline image 1]
On Mon, Feb 25, 2013 at 5:09 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote:
Dear Gari, The subfield module uses a different, independent method to segment the hippocampus, and consistency with ASEG results is not explicitly enforced. That said, the subfield module is inialialized with the ASEG, and the results should be pretty close to each other, for the most part. Have you visually inspected the segmentation for those cases in which the difference looks large? Thanks, /Eugenio
On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote:
Hi, I am calculating hippocampus volumes with 5.2 in CentOS 4.
I compare volumes (the same apply for lh and for rh) when calculating as:
Left.Hippocampus value in 1mm3 from aseg.stats I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and
obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in order to get mm3, and sum every column except left_hippocampal_fissure.
I obtain quite different values, for example:
row.names lh.aseg lhHIP rh.aseg rhHIP 1 S_00 4848.8 3828.187 4878.8 3767.739 2 S_02 4153.8 3371.517 4547.6 3389.918
Am I doing anything wrong? Should I calculate the hippos subfields volumes differently?
Many thanks! Gari _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
alveus (and fimbria) are defined to be part of the hippocampus in the aseg. Did you include them in your calculation of subfield hippocampal volume? On Tue, 26 Feb 2013, Joshua Lee wrote:
I have noticed that Freesurfer tends to include white matter in superior hippocampus (e.g. alveus), perhaps this is not included in the hipposubfields volumes?
Wondering, if I were to take a hand traced hippocampus rename it to aseg.mgz, and made sure that the label matched what Freesurfer expects, would the hipposubfields algorithm do its magic on this volume? Joshua
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Tue, Feb 26, 2013 at 9:48 AM, Garikoitz Lerma-Usabiaga garikoitz@gmail.com wrote: Thanks Juan Eugenio,we have visually inspected the segmentations, and we observe that the volume differences between aseg and hippo-subfields are constants among subjects, and consistent in both left and right hemispheres (please see table attached, columns diff.aseg.left.subfields and diff.aseg.right.subfields). Indeed, the percentage of the difference between the aseg and the hippo-subfields is about 20% average (19.5% for the left and 22.1% for the right hemisphere), and there are not strong differences at the individual subject level.
The aseg values always are bigger than the hippo-subfields across all planes (please see attached photos with some examples). And, as it can be seen in the attached pictures, the hippo-subfield segmentation seems to be more accurate than the aseg one.
We used the standard recon-all procedure with -hippo-subfields -qcache -all
Considering that these differences are pretty consistent across subjects, Do you think that there is anything wrong with our results? Or anything that we are missing in our analysis?
Thank you very much, Gari
Inline image 1
On Mon, Feb 25, 2013 at 5:09 PM, Juan Eugenio Iglesias iglesias@nmr.mgh.harvard.edu wrote: Dear Gari, The subfield module uses a different, independent method to segment the hippocampus, and consistency with ASEG results is not explicitly enforced. That said, the subfield module is inialialized with the ASEG, and the results should be pretty close to each other, for the most part. Have you visually inspected the segmentation for those cases in which the difference looks large? Thanks, /Eugenio
On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote: > Hi, > I am calculating hippocampus volumes with 5.2 in CentOS 4. > > > I compare volumes (the same apply for lh and for rh) when calculating > as: > > Left.Hippocampus value in 1mm3 from aseg.stats > > I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and > obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in > order to get mm3, and sum every column except > left_hippocampal_fissure. > > > I obtain quite different values, for example: > > row.names > lh.aseg > lhHIP > rh.aseg > rhHIP > 1 > S_00 > 4848.8 > 3828.187 > 4878.8 > 3767.739 > 2 > S_02 > 4153.8 > 3371.517 > 4547.6 > 3389.918 > > > Am I doing anything wrong? Should I calculate the hippos subfields > volumes differently? > > > > Many thanks! > Gari
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Bruce and Josh, the sum of all the hippo-subfields included all (the fimbria as well) except the fissure. We don't have hippo-subfields values related to the alveus (we run the standard command -hippo-subfields -all).
As suggested by Eugenio and Koen, we are going to use the -hippo-subfields values as we need the subfields volumes as well.
many thanks for your answers! Gari
On Tue, Feb 26, 2013 at 11:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
alveus (and fimbria) are defined to be part of the hippocampus in the aseg. Did you include them in your calculation of subfield hippocampal volume?
On Tue, 26 Feb 2013, Joshua Lee wrote:
I have noticed that Freesurfer tends to include white matter in superior
hippocampus (e.g. alveus), perhaps this is not included in the hipposubfields volumes?
Wondering, if I were to take a hand traced hippocampus rename it to aseg.mgz, and made sure that the label matched what Freesurfer expects, would the hipposubfields algorithm do its magic on this volume? Joshua
Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805
On Tue, Feb 26, 2013 at 9:48 AM, Garikoitz Lerma-Usabiaga < garikoitz@gmail.com> wrote: Thanks Juan Eugenio,we have visually inspected the segmentations, and we observe that the volume differences between aseg and
hippo-subfields are constants among subjects, and consistent inboth left and right hemispheres (please see table attached, columns diff.aseg.left.**subfields and diff.aseg.right.subfields). Indeed, the percentage of the difference between the aseg and the hippo-subfields is about 20% average (19.5% for the left and 22.1% for the right hemisphere), and there are not strong differences at the individual subject level.
The aseg values always are bigger than the hippo-subfields across all planes (please see attached photos with some examples). And, as it can be seen in the attached pictures, the hippo-subfield segmentation seems to be more accurate than the aseg one.
We used the standard recon-all procedure with -hippo-subfields -qcache -all
Considering that these differences are pretty consistent across subjects, Do you think that there is anything wrong with our results? Or anything that we are missing in our analysis?
Thank you very much, Gari
Inline image 1
On Mon, Feb 25, 2013 at 5:09 PM, Juan Eugenio Iglesias < iglesias@nmr.mgh.harvard.edu> wrote: Dear Gari, The subfield module uses a different, independent method to segment the hippocampus, and consistency with ASEG results is not explicitly enforced. That said, the subfield module is inialialized with the ASEG, and the results should be pretty close to each other, for the most part. Have you visually inspected the segmentation for those cases in which the difference looks large? Thanks, /Eugenio
On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote: > Hi, > I am calculating hippocampus volumes with 5.2 in CentOS 4. > > > I compare volumes (the same apply for lh and for rh) whencalculating > as: > > Left.Hippocampus value in 1mm3 from aseg.stats > > I use the method kvlQuantifyHippocampalSubfield**Segmentations.sh and > obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in > order to get mm3, and sum every column except > left_hippocampal_fissure. > > > I obtain quite different values, for example: > > row.names > lh.aseg > lhHIP > rh.aseg > rhHIP > 1 > S_00 > 4848.8 > 3828.187 > 4878.8 > 3767.739 > 2 > S_02 > 4153.8 > 3371.517 > 4547.6 > 3389.918 > > > Am I doing anything wrong? Should I calculate the hippos subfields > volumes differently? > > > > Many thanks! > Gari
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
------------------------------**------------------------------**
Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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/**compliancelinehttp://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.
______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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/**compliancelinehttp://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.
sure. Good luck Bruce On Sun, 3 Mar 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Bruce and Josh, the sum of all the hippo-subfields included all (the fimbria as well) except the fissure. We don't have hippo-subfields values related to the alveus (we run the standard command -hippo-subfields -all).
As suggested by Eugenio and Koen, we are going to use the -hippo-subfields values as we need the subfields volumes as well.
many thanks for your answers! Gari
On Tue, Feb 26, 2013 at 11:34 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: alveus (and fimbria) are defined to be part of the hippocampus in the aseg. Did you include them in your calculation of subfield hippocampal volume? On Tue, 26 Feb 2013, Joshua Lee wrote:
I have noticed that Freesurfer tends to include white matter in superior hippocampus (e.g. alveus), perhaps this is not included in the hipposubfields volumes? Wondering, if I were to take a hand traced hippocampus rename it to aseg.mgz, and made sure that the label matched what Freesurfer expects, would the hipposubfields algorithm do its magic on this volume? Joshua Joshua Lee Graduate Student Center for Mind and Brain & Department of Psychology University of California, Davis 530.747.3805 On Tue, Feb 26, 2013 at 9:48 AM, Garikoitz Lerma-Usabiaga <garikoitz@gmail.com> wrote:Thanks Juan Eugenio,we have visually inspected the segmentations, and we observe that the volume differences between aseg and hippo-subfields are constants among subjects, and consistent in both left and right hemispheres (please see table attached, columns diff.aseg.left.subfields and diff.aseg.right.subfields). Indeed, the percentage of the difference between the aseg and the hippo-subfields is about 20% average (19.5% for the left and 22.1% for the right hemisphere), and there are not strong differences at the individual subject level.
The aseg values always are bigger than the hippo-subfields across all planes (please see attached photos with some examples). And, as it can be seen in the attached pictures, the hippo-subfield segmentation seems to be more accurate than the aseg one.
We used the standard recon-all procedure with -hippo-subfields -qcache -all
Considering that these differences are pretty consistent across subjects, Do you think that there is anything wrong with our results? Or anything that we are missing in our analysis?
Thank you very much, Gari
Inline image 1
On Mon, Feb 25, 2013 at 5:09 PM, Juan Eugenio Iglesias iglesias@nmr.mgh.harvard.edu wrote: Dear Gari, The subfield module uses a different, independent method to segment the hippocampus, and consistency with ASEG results is not explicitly enforced. That said, the subfield module is inialialized with the ASEG, and the results should be pretty close to each other, for the most part. Have you visually inspected the segmentation for those cases in which the difference looks large? Thanks, /Eugenio
On Mon, 2013-02-25 at 14:10 +0100, Garikoitz Lerma-Usabiaga wrote: > Hi, > I am calculating hippocampus volumes with 5.2 in CentOS 4. > > > I compare volumes (the same apply for lh and for rh) when calculating > as: > > Left.Hippocampus value in 1mm3 from aseg.stats > > I use the method kvlQuantifyHippocampalSubfieldSegmentations.sh and > obtain the nonPartialVolumeStatsLeft.txt, divide each value by 8 in > order to get mm3, and sum every column except > left_hippocampal_fissure. > > > I obtain quite different values, for example: > > row.names > lh.aseg > lhHIP > rh.aseg > rhHIP > 1 > S_00 > 4848.8 > 3828.187 > 4878.8 > 3767.739 > 2 > S_02 > 4153.8 > 3371.517 > 4547.6 > 3389.918 > > > Am I doing anything wrong? Should I calculate the hippos subfields > volumes differently? > > > > Many thanks! > Gari
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias@nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology, MGH, Harvard Medical School 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Garikoitz Lerma-Usabiaga -
Joshua Lee -
Juan Eugenio Iglesias