Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
Hi Martin,
Unfortunately it is not a single subject, it happens to many. If I run FS 5.3, I also have to rerun the cross-sectional exploration study, otherwise differences between samples may be explained by different versions of the software. FYI, no editting was done, except for adjusting watershed parameters for a couple of subjects due to excessive skullstripping. After checking, i reran independent autorecon2+3, base + long for the affected pairs.
I'll get back to you when results of FS 5.3 are available.
Cheers, Cédric
On 6/28/13 2:43 AM, "Martin Reuter" <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Cedric,
Yes, that is too much difference. Something is going wrong. Is this a single subject or does it happen on many? Can you try FS 5.3 on the subject to see if that fixes it (in a different directory of course)?
It may also be that something goes wrong and needs edits. Or it could be that something got messed up by edits or re-running. So you could also process this subjects from scratch again (all tps cross, then base, then all tps long).
Best, Martin
On 06/25/2013 03:43 PM, Koolschijn, Cédric wrote: Hi Martin,
Thanks for your fast response. It makes sense that in the longi-stream results should be more reliable.
However, it worries me if I see segmentation differences up to 500%, for example amygdala volume going from 1475 to 503 Left and 1595 to 281 for Right, independent vs longitudinal stream respectively. In the current study we had a cross-sectional exploration study, followed by a longitudinal validation study (so two different samples). The above worries me if we want to compare the cross-sectional results with the longitudinal results, as the differences between independent and longitudinal are in a linear fashion.
Any thoughts on this?
Cheers, Cédric
From: Martin Reuter <mreuter@nmr.mgh.harvard.edumailto:mreuter@nmr.mgh.harvard.edu> Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn <P.C.M.P.Koolschijn@uva.nlmailto:P.C.M.P.Koolschijn@uva.nl> Cc: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
Hi Cedric,
this is as expected, the data changes when using the longitudinal stream (it will become more reliable, removing some of the variance you get in the independent processing). Becuase of the different processing approaches, the results from independent processing (cross) and long will not be directly comparable.
Cheers, Martin
On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote: Hi FreeSurfers,
I ran the longitudinal processing pipeline on my subjects, FS 5.0. Following the tutorial, first independently, then base, then long etc. Everything works well, no problems there.
Out of curiosity I compared the asegstats & aparcstats within subject at baseline (i.e. The same timepoint): so the independent fsid vs the same_fsid.long.same_fsid_template, and there are (large) differences between all volumes/thicknesses. The independent measures are in almost all brain areas larger compared to those derived from the longi-stream. Except for the IC, which is completely the same, but of course, this measure is based on the Buckner method and calculated differently.
Overall this seems a bit strange to me, because I believe there shouldn't be differences within subject on the same time-point. Is this the result of the within-subject template use for the longitudinal data or is something else going wrong, or is this normal?
Many thanks!
Cheers, Cédric
------------------------------------------------------------ P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Amsterdam, The Netherlands E P.C.M.P.Koolschijn@uva.nlmailto:P.C.M.P.Koolschijn@uva.nl W http://www.dutcharc.nl
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
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.
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
can you send us an example with a 500% increase? On Fri, 28 Jun 2013, Koolschijn, Cédric wrote:
Hi Martin,
Unfortunately it is not a single subject, it happens to many. If I run FS 5.3, I also have to rerun the cross-sectional exploration study, otherwise differences between samples may be explained by different versions of the software. FYI, no editting was done, except for adjusting watershed parameters for a couple of subjects due to excessive skullstripping. After checking, i reran independent autorecon2+3, base + long for the affected pairs.
I'll get back to you when results of FS 5.3 are available.
Cheers, Cédric
On 6/28/13 2:43 AM, "Martin Reuter" mreuter@nmr.mgh.harvard.edu wrote:
Hi Cedric, Yes, that is too much difference. Something is going wrong. Is this a single subject or does it happen on many? Can you try FS 5.3 on the subject to see if that fixes it (in a different directory of course)? It may also be that something goes wrong and needs edits. Or it could be that something got messed up by edits or re-running. So you could also process this subjects from scratch again (all tps cross, then base, then all tps long). Best, Martin On 06/25/2013 03:43 PM, Koolschijn, Cédric wrote: Hi Martin,Thanks for your fast response. It makes sense that in the longi-stream results should be more reliable.
However, it worries me if I see segmentation differences up to 500%, for example amygdala volume going from 1475 to 503 Left and 1595 to 281 for Right, independent vs longitudinal stream respectively. In the current study we had a cross-sectional exploration study, followed by a longitudinal validation study (so two different samples). The above worries me if we want to compare the cross-sectional results with the longitudinal results, as the differences between independent and longitudinal are in a linear fashion.
Any thoughts on this?
Cheers, Cédric
From: Martin Reuter mreuter@nmr.mgh.harvard.edu Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn P.C.M.P.Koolschijn@uva.nl Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
Hi Cedric, this is as expected, the data changes when using the longitudinal stream (it will become more reliable, removing some of the variance you get in the independent processing). Becuase of the different processing approaches, the results from independent processing (cross) and long will not be directly comparable. Cheers, Martin On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote: Hi FreeSurfers,I ran the longitudinal processing pipeline on my subjects, FS 5.0. Following the tutorial, first independently, then base, then long etc. Everything works well, no problems there.
Out of curiosity I compared the asegstats & aparcstats within subject at baseline (i.e. The same timepoint): so the independent fsid vs the same_fsid.long.same_fsid_template, and there are (large) differences between all volumes/thicknesses. The independent measures are in almost all brain areas larger compared to those derived from the longi-stream. Except for the IC, which is completely the same, but of course, this measure is based on the Buckner method and calculated differently.
Overall this seems a bit strange to me, because I believe there shouldn't be differences within subject on the same time-point. Is this the result of the within-subject template use for the longitudinal data or is something else going wrong, or is this normal?
Many thanks!
Cheers, Cédric
P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Amsterdam, The Netherlands E P.C.M.P.Koolschijn@uva.nl W http://www.dutcharc.nl
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listi nfo/freesurfer
It would be very interesting to know if this issue also happed in 5.3.
On Fri, Jun 28, 2013 at 1:28 PM, Koolschijn, Cédric < P.C.M.P.Koolschijn@uva.nl> wrote:
Hi Martin,
Unfortunately it is not a single subject, it happens to many. If I run FS 5.3, I also have to rerun the cross-sectional exploration study, otherwise differences between samples may be explained by different versions of the software. FYI, no editting was done, except for adjusting watershed parameters for a couple of subjects due to excessive skullstripping. After checking, i reran independent autorecon2+3, base + long for the affected pairs.
I'll get back to you when results of FS 5.3 are available.
Cheers, Cédric
On 6/28/13 2:43 AM, "Martin Reuter" mreuter@nmr.mgh.harvard.edu wrote:
Hi Cedric,
Yes, that is too much difference. Something is going wrong. Is this a single subject or does it happen on many? Can you try FS 5.3 on the subject to see if that fixes it (in a different directory of course)?
It may also be that something goes wrong and needs edits. Or it could be that something got messed up by edits or re-running. So you could also process this subjects from scratch again (all tps cross, then base, then all tps long).
Best, Martin
On 06/25/2013 03:43 PM, Koolschijn, Cédric wrote:
Hi Martin,
Thanks for your fast response. It makes sense that in the longi-stream results should be more reliable.
However, it worries me if I see segmentation differences up to 500%, for example amygdala volume going from 1475 to 503 Left and 1595 to 281 for Right, independent vs longitudinal stream respectively. In the current study we had a cross-sectional exploration study, followed by a longitudinal validation study (so two different samples). The above worries me if we want to compare the cross-sectional results with the longitudinal results, as the differences between independent and longitudinal are in a linear fashion.
Any thoughts on this?
Cheers, Cédric
From: Martin Reuter mreuter@nmr.mgh.harvard.edu Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn P.C.M.P.Koolschijn@uva.nl Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
Hi Cedric,
this is as expected, the data changes when using the longitudinal stream (it will become more reliable, removing some of the variance you get in the independent processing). Becuase of the different processing approaches, the results from independent processing (cross) and long will not be directly comparable.
Cheers, Martin
On 06/25/2013 04:02 AM, Koolschijn, Cédric wrote:
Hi FreeSurfers,
I ran the longitudinal processing pipeline on my subjects, FS 5.0. Following the tutorial, first independently, then base, then long etc. Everything works well, no problems there.
Out of curiosity I compared the asegstats & aparcstats within subject at baseline (i.e. The same timepoint): so the independent fsid vs the same_fsid.long.same_fsid_template, and there are (large) differences between all volumes/thicknesses. The independent measures are in almost all brain areas larger compared to those derived from the longi-stream. Except for the IC, which is completely the same, but of course, this measure is based on the Buckner method and calculated differently.
Overall this seems a bit strange to me, because I believe there shouldn't be differences within subject on the same time-point. Is this the result of the within-subject template use for the longitudinal data or is something else going wrong, or is this normal?
Many thanks!
Cheers, Cédric
P.C.M.P. Koolschijn (Cédric), PhD Dutch Autism & ADHD Research Center Brain and Cognition Amsterdam, The Netherlands *E *P.C.M.P.Koolschijn@uva.nl *W *http://www.dutcharc.nl
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
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.
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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@nmr.mgh.harvard.edu
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