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 mreu...@nmr.mgh.harvard.edumailto:mreu...@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 mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn p.c.m.p.koolsch...@uva.nlmailto:p.c.m.p.koolsch...@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.koolsch...@uva.nlmailto:p.c.m.p.koolsch...@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: mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edumailto:reu...@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
Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
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 mreu...@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 mreu...@nmr.mgh.harvard.edu Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn p.c.m.p.koolsch...@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.koolsch...@uva.nl W http://www.dutcharc.nl ___ Freesurfer mailing list freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listi nfo/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.
Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
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.koolsch...@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 mreu...@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 mreu...@nmr.mgh.harvard.edu Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn p.c.m.p.koolsch...@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.koolsch...@uva.nl *W *http://www.dutcharc.nl ___ Freesurfer mailing listfreesur...@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: mreu...@nmr.mgh.harvard.edu reu...@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
Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
This raises an interesting question. Given that the longitudinal process is more reliable, if we collect 2 scans on the same day, should we average those scans and then submit to Freesurfer or apply Freesurfer first and then create an average of the metrics from the longitudinal pipeline? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Jun 25, 2013 at 2:00 PM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: 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.koolsch...@uva.nl *W *http://www.dutcharc.nl ___ Freesurfer mailing listfreesur...@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: mreu...@nmr.mgh.harvard.edu reu...@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 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.
Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
You should take the better of the two images (the one without motion artifacts). Cheers, Martin On 06/26/2013 11:06 AM, MCLAREN, Donald wrote: This raises an interesting question. Given that the longitudinal process is more reliable, if we collect 2 scans on the same day, should we average those scans and then submit to Freesurfer or apply Freesurfer first and then create an average of the metrics from the longitudinal pipeline? Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren http://www.martinos.org/%7Emclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Jun 25, 2013 at 2:00 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu wrote: 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.koolsch...@uva.nl mailto:p.c.m.p.koolsch...@uva.nl /W /http://www.dutcharc.nl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://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 tel:%2B1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edu mailto:reu...@mit.edu Web :http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
[Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
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.koolsch...@uva.nlmailto:p.c.m.p.koolsch...@uva.nl W http://www.dutcharc.nl ___ 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.
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.koolsch...@uva.nl mailto:p.c.m.p.koolsch...@uva.nl /W /http://www.dutcharc.nl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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: mreu...@nmr.mgh.harvard.edu reu...@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.
Re: [Freesurfer] Differences on baseline volumes within subject cross-sectional vs longitudinal processing
Hi Martin, Thanks for your fast response. Apologies for the second email, I forgot to include the mailinglist. 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 mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu Date: Tuesday, June 25, 2013 8:00 PM To: Cédric Koolschijn p.c.m.p.koolsch...@uva.nlmailto:p.c.m.p.koolsch...@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.koolsch...@uva.nlmailto:p.c.m.p.koolsch...@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: mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edumailto:reu...@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. ___ 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.
