Hi everyone!
I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks!
Jessica Liu
This is not normal. Maybe you should check the aseg volume for improper segmentation.
On Thu, Jun 23, 2011 at 19:27, Jessica Liu jessicaliu92@gmail.com wrote:
Hi everyone!
I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks!
Jessica Liu
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.
Looking at the scans (attached, 3T on the left and 1.5T on the right, yellow hippocampus), I think you've made a good point. More comments are much appreciated, thanks!
Jessica Liu
2011/6/23 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br
This is not normal. Maybe you should check the aseg volume for improper segmentation.
On Thu, Jun 23, 2011 at 19:27, Jessica Liu jessicaliu92@gmail.com wrote:
Hi everyone!
I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks!
Jessica Liu
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 Jessica,
the 1.5t scan looks kind of washed out and low contrast, but of course it's hard to tell from an image. The 3T looks much crisper. Were the sequence parameters matched? I'm not sure what you're trying to show with this. The 3T multi-channel scan will have a much, much higher SNR than the 1.5T single channel, so the results will not at all be comparable.
Bruce
On Thu, 23 Jun 2011, Jessica Liu wrote:
Looking at the scans (attached, 3T on the left and 1.5T on the right, yellow hippocampus), I think you've made a good point. More comments are much appreciated, thanks!
Jessica Liu
2011/6/23 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br This is not normal. Maybe you should check the aseg volume for improper segmentation.
On Thu, Jun 23, 2011 at 19:27, Jessica Liu jessicaliu92@gmail.com wrote: Hi everyone!
I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks!
Jessica Liu
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 Dr. Fischl,
Thanks for your comments. The aim of my study is to analyze the brain volume in AD subjects. Most of the study was scanned on the 1.5T (single-channel head coil) with a few subjects rescanned on the 3T (12-channel head coil), so we would like to compare the brain volume of the same subject on both scanners. In addition, the protocols on the two scanners didn't match exactly due to the limitations of our over 15-years-old 1.5T scanner (i.e. non-isotropic voxel size). From your comment, I gather that the 1.5T data is rather imprecise/unreliable. Since I'm a summer student, do you recommend that I should concentrate on analyzing the 3T data only, and hopefully all of the subjects can be rescanned on the 3T? Thanks!
Jessica Liu
2011/6/23 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Jessica,
the 1.5t scan looks kind of washed out and low contrast, but of course it's hard to tell from an image. The 3T looks much crisper. Were the sequence parameters matched? I'm not sure what you're trying to show with this. The 3T multi-channel scan will have a much, much higher SNR than the 1.5T single channel, so the results will not at all be comparable.
Bruce
On Thu, 23 Jun 2011, Jessica Liu wrote:
Looking at the scans (attached, 3T on the left and 1.5T on the right,
yellow hippocampus), I think you've made a good point. More comments are much appreciated, thanks!
Jessica Liu
2011/6/23 Pedro Paulo de Magalhães Oliveira Junior ppj@netfilter.com.br This is not normal. Maybe you should check the aseg volume for improper segmentation.
On Thu, Jun 23, 2011 at 19:27, Jessica Liu jessicaliu92@gmail.com wrote: Hi everyone!
I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks!
Jessica Liu
______________________________**_________________ 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.
Hi Jessica
yes, probably. With so many differences (sequence, field strength, coil) it will be really hard to get anything out of a combined dataset.
sorry Bruce On Fri, 24 Jun 2011, Jessica Liu wrote:
Hi Dr. Fischl,
Thanks for your comments. The aim of my study is to analyze the brain volume in AD subjects. Most of the study was scanned on the 1.5T (single-channel head coil) with a few subjects rescanned on the 3T (12-channel head coil), so we would like to compare the brain volume of the same subject on both scanners. In addition, the protocols on the two scanners didn't match exactly due to the limitations of our over 15-years-old 1.5T scanner (i.e. non-isotropic voxel size). From your comment, I gather that the 1.5T data is rather imprecise/unreliable. Since I'm a summer student, do you recommend that I should concentrate on analyzing the 3T data only, and hopefully all of the subjects can be rescanned on the 3T? Thanks!
Jessica Liu
2011/6/23 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Jessica,
the 1.5t scan looks kind of washed out and low contrast, but of course it's hard to tell from an image. The 3T looks much crisper. Were the sequence parameters matched? I'm not sure what you're trying to show with this. The 3T multi-channel scan will have a much, much higher SNR than the 1.5T single channel, so the results will not at all be comparable. Bruce On Thu, 23 Jun 2011, Jessica Liu wrote: Looking at the scans (attached, 3T on the left and 1.5T on the right, yellow hippocampus), I think you've made a good point. More comments are much appreciated, thanks! Jessica Liu 2011/6/23 Pedro Paulo de Magalhães Oliveira Junior <ppj@netfilter.com.br> This is not normal. Maybe you should check the aseg volume for improper segmentation. On Thu, Jun 23, 2011 at 19:27, Jessica Liu <jessicaliu92@gmail.com> wrote: Hi everyone! I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks! Jessica Liu _______________________________________________ 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.
Alright, thanks for all of your input!
Jessica
2011/6/24 Bruce Fischl fischl@nmr.mgh.harvard.edu
Hi Jessica
yes, probably. With so many differences (sequence, field strength, coil) it will be really hard to get anything out of a combined dataset.
sorry Bruce
On Fri, 24 Jun 2011, Jessica Liu wrote:
Hi Dr. Fischl,
Thanks for your comments. The aim of my study is to analyze the brain volume in AD subjects. Most of the study was scanned on the 1.5T (single-channel head coil) with a few subjects rescanned on the 3T (12-channel head coil), so we would like to compare the brain volume of the same subject on both scanners. In addition, the protocols on the two scanners didn't match exactly due to the limitations of our over 15-years-old 1.5T scanner (i.e. non-isotropic voxel size). From your comment, I gather that the 1.5T data is rather imprecise/unreliable. Since I'm a summer student, do you recommend that I should concentrate on analyzing the 3T data only, and hopefully all of the subjects can be rescanned on the 3T? Thanks!
Jessica Liu
2011/6/23 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Jessica,
the 1.5t scan looks kind of washed out and low contrast, but of course it's hard to tell from an image. The 3T looks much crisper. Were the sequence parameters matched? I'm not sure what you're trying to show with this. The 3T multi-channel scan will have a much, much higher SNR than the 1.5T single channel, so the results will not at all be comparable. Bruce On Thu, 23 Jun 2011, Jessica Liu wrote: Looking at the scans (attached, 3T on the left and 1.5T on the right, yellow hippocampus), I think you've made a good point. More comments are much appreciated, thanks! Jessica Liu 2011/6/23 Pedro Paulo de Magalhães Oliveira Junior <ppj@netfilter.com.br> This is not normal. Maybe you should check the aseg volume for improper segmentation. On Thu, Jun 23, 2011 at 19:27, Jessica Liu <jessicaliu92@gmail.com> wrote: Hi everyone! I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks! Jessica Liu ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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 Jessica,
what were the coils? Certainly you will find substantial differences comparing across both field strength and receive coil. Did the segmentations look reasonable? Was it the same sequence?
Bruce
On Thu, 23 Jun 2011, Jessica Liu wrote:
Hi everyone!
I'm currently a summer student working at a lab which uses Freesurfer to measure hippocampal volumes. I noticed that scanning the same patient first on a GE 3T (Multi-channel head coil) and then a GE 1.5T (single-channel head coil) 24 hours later resulted in a 30% increase in the left hippocampus volume and a 18% increase for the right hippocampus based on the values in aseg.stats. Can anyone please comment on this and explain the large discrepancies? Thanks!
Jessica Liu
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Jessica Liu -
Pedro Paulo de Magalhães Oliveira Junior