Hi all,
I have a dataset with AD patients that were scanned twice, once at 1.5T and once at 3T at an interval of a few years. The ICV values are lower for almost all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions supposed to be independent of brain volume as it is based on a scaling factor derived from the Tailairach transform of the skull? Many thanks!
Cheers,
Diederick
Dear Diederick,
were all subjects acquired at point 1 with 1.5T and at point 2 with 3T? Or was the same subject acquired with the same scanner at both timepoints? In the first case, could it be simply a problem of scanner-related variability of ICV assessment (different scanner different sequence parameters different performance in assessing ICV)?
Regards,
Paola Valsasina
_____
Da: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Per conto di Diederick Stoffers Inviato: lunedì 20 dicembre 2010 12.49 A: Freesurfer List Oggetto: [Freesurfer] ICV differs systematically in repeated measurements
Hi all,
I have a dataset with AD patients that were scanned twice, once at 1.5T and once at 3T at an interval of a few years. The ICV values are lower for almost all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions supposed to be independent of brain volume as it is based on a scaling factor derived from the Tailairach transform of the skull? Many thanks!
Cheers,
Diederick
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Hi Diederick,
In a longitudinal study you need to ensure identical acquisition and processing, else you'll introduce a systematic bias. Some of my recent analyses indicate that even updating the software on the scanner can bias your results. Hardware changes are worse.
Best Martin
On Dec 20, 2010, at 6:48 AM, Diederick Stoffers d.stoffers@gmail.com wrote:
Hi all,
I have a dataset with AD patients that were scanned twice, once at 1.5T and once at 3T at an interval of a few years. The ICV values are lower for almost all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions supposed to be independent of brain volume as it is based on a scaling factor derived from the Tailairach transform of the skull? Many thanks!
Cheers,
Diederick _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This is just a thought, but is this issue mitigated to some degree if you can show that the regions in which you are interested meet a certain minimum signal to noise ratio? Or maybe a more stringent requirement would be necessary, such that the SNR of the ROIs don't differ significantly?
Always wondered about this.
Anthony
On 12/20/10 9:26 AM, Martin Reuter wrote:
Hi Diederick,
In a longitudinal study you need to ensure identical acquisition and processing, else you'll introduce a systematic bias. Some of my recent analyses indicate that even updating the software on the scanner can bias your results. Hardware changes are worse.
Best Martin
On Dec 20, 2010, at 6:48 AM, Diederick Stoffersd.stoffers@gmail.com wrote:
Hi all,
I have a dataset with AD patients that were scanned twice, once at 1.5T and once at 3T at an interval of a few years. The ICV values are lower for almost all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions supposed to be independent of brain volume as it is based on a scaling factor derived from the Tailairach transform of the skull? Many thanks!
Cheers,
Diederick _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Anthony,
I don't think so. The problem is that the fundamental T1 contrast is different at 3T than att 1.5T, which results in systematic biases.
cheers Bruce On Mon, 20 Dec 2010, Anthony Dick wrote:
This is just a thought, but is this issue mitigated to some degree if you can show that the regions in which you are interested meet a certain minimum signal to noise ratio? Or maybe a more stringent requirement would be necessary, such that the SNR of the ROIs don't differ significantly?
Always wondered about this.
Anthony
On 12/20/10 9:26 AM, Martin Reuter wrote:
Hi Diederick,
In a longitudinal study you need to ensure identical acquisition and processing, else you'll introduce a systematic bias. Some of my recent analyses indicate that even updating the software on the scanner can bias your results. Hardware changes are worse.
Best Martin
On Dec 20, 2010, at 6:48 AM, Diederick Stoffersd.stoffers@gmail.com wrote:
Hi all,
I have a dataset with AD patients that were scanned twice, once at 1.5T and once at 3T at an interval of a few years. The ICV values are lower for almost all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions supposed to be independent of brain volume as it is based on a scaling factor derived from the Tailairach transform of the skull? Many thanks!
Cheers,
Diederick _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Would this problem also apply for fMRI or diffusion weighted scanning?
On 12/20/10 10:41 AM, Bruce Fischl wrote:
Hi Anthony,
I don't think so. The problem is that the fundamental T1 contrast is different at 3T than att 1.5T, which results in systematic biases.
cheers Bruce On Mon, 20 Dec 2010, Anthony Dick wrote:
This is just a thought, but is this issue mitigated to some degree if you can show that the regions in which you are interested meet a certain minimum signal to noise ratio? Or maybe a more stringent requirement would be necessary, such that the SNR of the ROIs don't differ significantly?
Always wondered about this.
Anthony
On 12/20/10 9:26 AM, Martin Reuter wrote:
Hi Diederick,
In a longitudinal study you need to ensure identical acquisition and processing, else you'll introduce a systematic bias. Some of my recent analyses indicate that even updating the software on the scanner can bias your results. Hardware changes are worse.
Best Martin
On Dec 20, 2010, at 6:48 AM, Diederick Stoffersd.stoffers@gmail.com wrote:
Hi all,
I have a dataset with AD patients that were scanned twice, once at 1.5T and once at 3T at an interval of a few years. The ICV values are lower for almost all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions supposed to be independent of brain volume as it is based on a scaling factor derived from the Tailairach transform of the skull? Many thanks!
Cheers,
Diederick _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
probably. The T2* will be different, so you'll have a different TE and different contrast, SNR and CNR On Mon, 20 Dec 2010, Anthony Dick wrote:
Would this problem also apply for fMRI or diffusion weighted scanning?
On 12/20/10 10:41 AM, Bruce Fischl wrote:
Hi Anthony,
I don't think so. The problem is that the fundamental T1 contrast is different at 3T than att 1.5T, which results in systematic biases.
cheers Bruce On Mon, 20 Dec 2010, Anthony Dick wrote:
This is just a thought, but is this issue mitigated to some degree if you can show that the regions in which you are interested meet a certain minimum signal to noise ratio? Or maybe a more stringent requirement would be necessary, such that the SNR of the ROIs don't differ significantly?
Always wondered about this.
Anthony
On 12/20/10 9:26 AM, Martin Reuter wrote:
Hi Diederick,
In a longitudinal study you need to ensure identical acquisition and processing, else you'll introduce a systematic bias. Some of my recent analyses indicate that even updating the software on the scanner can bias your results. Hardware changes are worse.
Best Martin
On Dec 20, 2010, at 6:48 AM, Diederick Stoffersd.stoffers@gmail.com wrote:
Hi all,
I have a dataset with AD patients that were scanned twice, once at 1.5T and once at 3T at an interval of a few years. The ICV values are lower for almost all subjects at timepoint two (FS 5.0). Isn't ICV in the later FS versions supposed to be independent of brain volume as it is based on a scaling factor derived from the Tailairach transform of the skull? Many thanks!
Cheers,
Diederick _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
-
Anthony Dick -
Bruce Fischl -
Diederick Stoffers -
Martin Reuter -
Paola Valsasina