Dear FreeSurfer export,
I have used the longitudinal stream in FreeSurfer. However, when I extracted the ICV for adolescents and young adult, I get the same number for those subjects that are present at two-time points. Will registration to a common space cause the change in ICV? Can this change explain why the icv is equal at 15 and 19 years of age for all my subjects with two-time points?
Best regards,
Knut Jørgen Bjuland PhD candidate NTNU Trondheim
Hi Knut,
the longitudinal stream assumes head size is fixed across time. That is why we report only one ICV (the one from the within subject template) in all time points. If in your data heads are growing still, you can still use the longitudinal stream, but need to be carefully inspecting your data (e.g. are surfaces OK in both time points, is the skull strip good etc). You can also read out the individual ICV on each time point when looking at the cross sectional directories (first step of the long pipeline), there in aseg. stats are the ICV's for each time point.
Best, Martin
On 10/13/2014 12:24 PM, Knut J Bjuland wrote:
Dear FreeSurfer export,
I have used the longitudinal stream in FreeSurfer. However, when I extracted the ICV for adolescents and young adult, I get the same number for those subjects that are present at two-time points. Will registration to a common space cause the change in ICV? Can this change explain why the icv is equal at 15 and 19 years of age for all my subjects with two-time points?
Best regards,
Knut Jørgen Bjuland PhD candidate NTNU Trondheim
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Martin and FS experts,
I have a small follow-up question regarding the post below. Given a young sample where ICV is still growing, that I want to control for this and that the data look ok: Can I use the cross-sectional ICV as a covariate in analyses on the longitudinal data? Or will this introduce any bias?
In other words, does “the longitudinal stream assumes head size is fixed across time” affect the estimated long values when this assumption is incorrect?
Best regards, Christian K Tamnes
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Reuter mreuter@nmr.mgh.harvard.edu Sent: 14 October 2014 17:23 To: Freesurfer support list Subject: Re: [Freesurfer] ICV for adolescent and young adult in longitudinal stream
Hi Knut,
the longitudinal stream assumes head size is fixed across time. That is why we report only one ICV (the one from the within subject template) in all time points. If in your data heads are growing still, you can still use the longitudinal stream, but need to be carefully inspecting your data (e.g. are surfaces OK in both time points, is the skull strip good etc). You can also read out the individual ICV on each time point when looking at the cross sectional directories (first step of the long pipeline), there in aseg. stats are the ICV's for each time point.
Best, Martin
On 10/13/2014 12:24 PM, Knut J Bjuland wrote:
Dear FreeSurfer export,
I have used the longitudinal stream in FreeSurfer. However, when I extracted the ICV for adolescents and young adult, I get the same number for those subjects that are present at two-time points. Will registration to a common space cause the change in ICV? Can this change explain why the icv is equal at 15 and 19 years of age for all my subjects with two-time points?
Best regards,
Knut Jørgen Bjuland PhD candidate NTNU Trondheim
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Martin Reuter
Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
_______________________________________________ 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 Christian,
Yes, you can use the ICV from the cross-sectional processing as co-variate. The longitudinal stream assumes head-size is not changing much in a few steps, but is still relatively robust in capturing large brain changes. I have never tested it thoroughly in kids and am not sure what effect it has there. These things could happen: - you may need to do more editing (skull strip and control points) as usual. - you may see cases that fail and edits don't help much - many cases probably work fine unless head size grows a lot
The longitudinal stream is not designed for growing heads and so inspection is key. If you find a case where it fails and editing does not fix it, let me know. I will be working on extensions and these cases are valuable for fine tuning and testing. Also in the worst case (if longitudinal fails too often) simply use the cross sectional (independently processed) results for all subjects and time point.
Best, Martin
On 10/27/2014 05:59 AM, Christian Krog Tamnes wrote:
Dear Martin and FS experts,
I have a small follow-up question regarding the post below. Given a young sample where ICV is still growing, that I want to control for this and that the data look ok: Can I use the cross-sectional ICV as a covariate in analyses on the longitudinal data? Or will this introduce any bias?
In other words, does “the longitudinal stream assumes head size is fixed across time” affect the estimated long values when this assumption is incorrect?
Best regards, Christian K Tamnes
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Martin Reuter mreuter@nmr.mgh.harvard.edu Sent: 14 October 2014 17:23 To: Freesurfer support list Subject: Re: [Freesurfer] ICV for adolescent and young adult in longitudinal stream
Hi Knut,
the longitudinal stream assumes head size is fixed across time. That is why we report only one ICV (the one from the within subject template) in all time points. If in your data heads are growing still, you can still use the longitudinal stream, but need to be carefully inspecting your data (e.g. are surfaces OK in both time points, is the skull strip good etc). You can also read out the individual ICV on each time point when looking at the cross sectional directories (first step of the long pipeline), there in aseg. stats are the ICV's for each time point.
Best, Martin
On 10/13/2014 12:24 PM, Knut J Bjuland wrote:
Dear FreeSurfer export,
I have used the longitudinal stream in FreeSurfer. However, when I extracted the ICV for adolescents and young adult, I get the same number for those subjects that are present at two-time points. Will registration to a common space cause the change in ICV? Can this change explain why the icv is equal at 15 and 19 years of age for all my subjects with two-time points?
Best regards,
Knut Jørgen Bjuland PhD candidate NTNU Trondheim
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Dr. Martin Reuter
Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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
freesurfer@nmr.mgh.harvard.edu
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Knut J Bjuland -
Martin Reuter