Hi,
I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images?
Thank you
Dorsa Ghaffari
Hi Dorsa,
until version 6 of FreeSurfer is released you could try to follow the HiResRecon (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon) which should enable you to process the data in its native resolution. With FreeSurfer v6 this workaround will not be necessary anymore, as the processing pipeline has been updated. If you want to, you could also try out a recent developer build. However, it is still under development.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Dorsa Haji Ghaffari Gesendet: Dienstag, 19. Juli 2016 18:06 An: Freesurfer support list Betreff: [Freesurfer] question about voxel size
Hi,
I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images?
Thank you
Dorsa Ghaffari
Hi Dorsa
are they really that highres? Sometimes people do zero-padding and Fourier interpolation on the scanner. 1/2mm cubic is pushing the resolution and if they are really that high res they will be either very noisy or very long scans (or both)
cheers Bruce
On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images?
Thank you
Dorsa Ghaffari
Hi Bruce,
The original 3TS images have 1mm^3 resolution, but we resample and co-register them to our CT scans and the resulting image has a higher resolution. My problem now is that the volume of the left thalamus segmented out by Freesurfer is half of the volume of the thalamus traced manually by one of my labmates. Do you have any guesses on why is this happening?
Thank you
Dorsa
On Tue, Jul 19, 2016 at 1:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dorsa
are they really that highres? Sometimes people do zero-padding and Fourier interpolation on the scanner. 1/2mm cubic is pushing the resolution and if they are really that high res they will be either very noisy or very long scans (or both)
cheers Bruce
On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
Hi,
I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images?
Thank you
Dorsa Ghaffari
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 Dorsa
why not give the original 1mm scans to freesurfer, then upsample the segmented images? And no, I wouldn't venture a guess without seeing the data Bruce
On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
Hi Bruce, The original 3TS images have 1mm^3 resolution, but we resample and co-register them to our CT scans and the resulting image has a higher resolution. My problem now is that the volume of the left thalamus segmented out by Freesurfer is half of the volume of the thalamus traced manually by one of my labmates. Do you have any guesses on why is this happening?
Thank you
Dorsa
On Tue, Jul 19, 2016 at 1:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Dorsa
are they really that highres? Sometimes people do zero-padding and Fourier interpolation on the scanner. 1/2mm cubic is pushing the resolution and if they are really that high res they will be either very noisy or very long scans (or both) cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images? Thank you Dorsa Ghaffari
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.
Yes That is a possible and I am going to talk to my group about it. I have attached the brain segmentation and the aseg.stats. I'll be happy to hear any comments about the thalamus size.
Thank you
Dorsa
On Tue, Jul 19, 2016 at 2:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dorsa
why not give the original 1mm scans to freesurfer, then upsample the segmented images? And no, I wouldn't venture a guess without seeing the data
Bruce
On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
Hi Bruce,
The original 3TS images have 1mm^3 resolution, but we resample and co-register them to our CT scans and the resulting image has a higher resolution. My problem now is that the volume of the left thalamus segmented out by Freesurfer is half of the volume of the thalamus traced manually by one of my labmates. Do you have any guesses on why is this happening?
Thank you
Dorsa
On Tue, Jul 19, 2016 at 1:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Dorsa
are they really that highres? Sometimes people do zero-padding and Fourier interpolation on the scanner. 1/2mm cubic is pushing the resolution and if they are really that high res they will be either very noisy or very long scans (or both) cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images? Thank you Dorsa Ghaffari
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 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 Dorsa
without the norm.mgz I have no way to evaluate the accuracy of the aseg.
cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
Yes That is a possible and I am going to talk to my group about it. I have attached the brain segmentation and the aseg.stats. I'll be happy to hear any comments about the thalamus size.
Thank you
Dorsa
On Tue, Jul 19, 2016 at 2:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Dorsa
why not give the original 1mm scans to freesurfer, then upsample the segmented images? And no, I wouldn't venture a guess without seeing the data Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi Bruce, The original 3TS images have 1mm^3 resolution, but we resample and co-register them to our CT scans and the resulting image has a higher resolution. My problem now is that the volume of the left thalamus segmented out by Freesurfer is half of the volume of the thalamus traced manually by one of my labmates. Do you have any guesses on why is this happening? Thank you Dorsa On Tue, Jul 19, 2016 at 1:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Dorsa are they really that highres? Sometimes people do zero-padding and Fourier interpolation on the scanner. 1/2mm cubic is pushing the resolution and if they are really that high res they will be either very noisy or very long scans (or both) cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images? Thank you Dorsa Ghaffari _______________________________________________ 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 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.
Here it is. Also can you explain why the algorithm works best with 1mm^3 voxel size?
Thank you!
On Tue, Jul 19, 2016 at 4:06 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Dorsa
without the norm.mgz I have no way to evaluate the accuracy of the aseg.
cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
Yes That is a possible and I am going to talk to my group about it. I have
attached the brain segmentation and the aseg.stats. I'll be happy to hear any comments about the thalamus size.
Thank you
Dorsa
On Tue, Jul 19, 2016 at 2:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote: Hi Dorsa
why not give the original 1mm scans to freesurfer, then upsample the segmented images? And no, I wouldn't venture a guess without seeing the data Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi Bruce, The original 3TS images have 1mm^3 resolution, but we resample and co-register them to our CT scans and the resulting image has a higher resolution. My problem now is that the volume of the left thalamus segmented out by Freesurfer is half of the volume of the thalamus traced manually by one of my labmates. Do you have any guesses on why is this happening? Thank you Dorsa On Tue, Jul 19, 2016 at 1:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Dorsa are they really that highres? Sometimes people do zero-padding and Fourier interpolation on the scanner. 1/2mm cubic is pushing the resolution and if they are really that high res they will be either very noisy or very long scans (or both) cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images? Thank you Dorsa Ghaffari _______________________________________________ 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 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 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 Dorsa
it works best with 1mm data as that was what it was designed for. Higher res can reveal unmodeled structures (e.g. stria of Gennari) that make things less accurate
cheers Bruce
On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote:
Here it is. Also can you explain why the algorithm works best with 1mm^3 voxel size?
Thank you!
On Tue, Jul 19, 2016 at 4:06 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Dorsa
without the norm.mgz I have no way to evaluate the accuracy of the aseg. cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Yes That is a possible and I am going to talk to my group about it. I have attached the brain segmentation and the aseg.stats. I'll be happy to hear any comments about the thalamus size. Thank you Dorsa On Tue, Jul 19, 2016 at 2:08 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Dorsa why not give the original 1mm scans to freesurfer, then upsample the segmented images? And no, I wouldn't venture a guess without seeing the data Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi Bruce, The original 3TS images have 1mm^3 resolution, but we resample and co-register them to our CT scans and the resulting image has a higher resolution. My problem now is that the volume of the left thalamus segmented out by Freesurfer is half of the volume of the thalamus traced manually by one of my labmates. Do you have any guesses on why is this happening? Thank you Dorsa On Tue, Jul 19, 2016 at 1:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Dorsa are they really that highres? Sometimes people do zero-padding and Fourier interpolation on the scanner. 1/2mm cubic is pushing the resolution and if they are really that high res they will be either very noisy or very long scans (or both) cheers Bruce On Tue, 19 Jul 2016, Dorsa Haji Ghaffari wrote: Hi, I have a T1 weighted MRI which I want to segment using Freesurfer. The voxel sizes are 0.48*0.48*0.48. I read that the ideal voxel size for freesurfer is 1mm^3. Is there any manual adjustments that I can make to get good results with my 0.48 voxel size images? Thank you Dorsa Ghaffari _______________________________________________ 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 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 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 -
Dorsa Haji Ghaffari -
Falk Lüsebrink