External Email - Use Caution
Dear FreeSurfer Team,
We are analyzing some longitudinal data (baseline [0], 6 months, 1 year, 1.5 years) using FreeSurfer 7.4.1. We already analyzed two timepoints (basline[0] and 6 months) but now we are trying to look at 4 timepoints in total.
I was wondering what the best way would be to do this. For the longitudinal processing, should we create 3 bases/within-subject templates between 0-6 months (this is already done), 0-1year, 0-1.5years), or between 0-6months, 6months-1year, 1year-1.5years. Or both?
Also, is it okay to correct/edit only the bases?
After the longitudinal processing, can we create a Longitudinal Table and apply the two-stage model (LongitudinalTwoStageModel) method? Or because of the 4 time points, we need to apply something else.
Thank you for your help in advance!
All the best, Eszter
Here is the tutorial for longitudinal processing - https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
The 'base' and 'long' steps of the longitudinal processing should be re-run after adding new timepoints.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Eszter Boros Sent: Wednesday, January 15, 2025 1:52 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] longitudinal analyses, more than 2 timepoints
External Email - Use Caution Dear FreeSurfer Team,
We are analyzing some longitudinal data (baseline [0], 6 months, 1 year, 1.5 years) using FreeSurfer 7.4.1. We already analyzed two timepoints (basline[0] and 6 months) but now we are trying to look at 4 timepoints in total.
I was wondering what the best way would be to do this. For the longitudinal processing, should we create 3 bases/within-subject templates between 0-6 months (this is already done), 0-1year, 0-1.5years), or between 0-6months, 6months-1year, 1year-1.5years. Or both?
Also, is it okay to correct/edit only the bases?
After the longitudinal processing, can we create a Longitudinal Table and apply the two-stage model (LongitudinalTwoStageModel) method? Or because of the 4 time points, we need to apply something else.
Thank you for your help in advance!
All the best, Eszter
External Email - Use Caution
Thank you for the quick response! I appreciate it. I am not sure what you mean by rerun specifically. Should I rerun separate analyses for 0-6 months, 0-1year, and 0-1.5 years? Or can I analyze all of them in the same model? I do not think I should rerun 0-6months if that is already analyzed, right? Thank you!
Huang, Yujing YHUANG43@mgh.harvard.edu ezt írta (időpont: 2025. jan. 15., Sze, 16:20):
Here is the tutorial for longitudinal processing - https://secure-web.cisco.com/1i3PDR08oGR9V8EyN5vNTRW6mNleyQB69JGWx-o-GpV4uK3...
The 'base' and 'long' steps of the longitudinal processing should be re-run after adding new timepoints.
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Eszter Boros *Sent:* Wednesday, January 15, 2025 1:52 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] longitudinal analyses, more than 2 timepoints
External Email - Use Caution *Dear FreeSurfer Team,
We are analyzing some longitudinal data (baseline [0], 6 months, 1 year, 1.5 years) using FreeSurfer 7.4.1. We already analyzed two timepoints (basline[0] and 6 months) but now we are trying to look at 4 timepoints in total.
I was wondering what the best way would be to do this. For the longitudinal processing, should we create 3 bases/within-subject templates between 0-6 months (this is already done), 0-1year, 0-1.5years), or between 0-6months, 6months-1year, 1year-1.5years. Or both?
Also, is it okay to correct/edit only the bases?
After the longitudinal processing, can we create a Longitudinal Table and apply the two-stage model (LongitudinalTwoStageModel) method? Or because of the 4 time points, we need to apply something else.
Thank you for your help in advance!
All the best, Eszter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1PhuPIEywVGSr6qRjuqsyLX2vz6twVAkF8deA2SrN4CZ-xK... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1Mn0xkezd14ZminLzCFO740AbxLEnwthdz81snVi3lg9VhG... < https://secure-web.cisco.com/1Mn0xkezd14ZminLzCFO740AbxLEnwthdz81snVi3lg9VhG... .
External Email - Use Caution
I apologize! I think I have just realized that I can create one base based on 4 time points, right?
recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -tp <tp3id> -tp <tp4id> -all
Thank you!
Eszter Boros boros.eszter0226@gmail.com ezt írta (időpont: 2025. jan. 17., P, 12:55):
Thank you for the quick response! I appreciate it. I am not sure what you mean by rerun specifically. Should I rerun separate analyses for 0-6 months, 0-1year, and 0-1.5 years? Or can I analyze all of them in the same model? I do not think I should rerun 0-6months if that is already analyzed, right? Thank you!
Huang, Yujing YHUANG43@mgh.harvard.edu ezt írta (időpont: 2025. jan. 15., Sze, 16:20):
Here is the tutorial for longitudinal processing - https://secure-web.cisco.com/15H1lCCgBPzjRd89RtWHk9KzzXEM40qS4p5I4M8lLImOuIL...
The 'base' and 'long' steps of the longitudinal processing should be re-run after adding new timepoints.
Yujing
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Eszter Boros *Sent:* Wednesday, January 15, 2025 1:52 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] longitudinal analyses, more than 2 timepoints
External Email - Use Caution *Dear FreeSurfer Team,
We are analyzing some longitudinal data (baseline [0], 6 months, 1 year, 1.5 years) using FreeSurfer 7.4.1. We already analyzed two timepoints (basline[0] and 6 months) but now we are trying to look at 4 timepoints in total.
I was wondering what the best way would be to do this. For the longitudinal processing, should we create 3 bases/within-subject templates between 0-6 months (this is already done), 0-1year, 0-1.5years), or between 0-6months, 6months-1year, 1year-1.5years. Or both?
Also, is it okay to correct/edit only the bases?
After the longitudinal processing, can we create a Longitudinal Table and apply the two-stage model (LongitudinalTwoStageModel) method? Or because of the 4 time points, we need to apply something else.
Thank you for your help in advance!
All the best, Eszter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1VnOtHaDxJ2OrtICt27VxI5KsyGvyE4zZcz2geKvcTAKUof... 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 Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1onxNuFESdAX_xYJxmT4easbFRV652AbsGLW8n0ac7H2FlQ... < https://secure-web.cisco.com/1onxNuFESdAX_xYJxmT4easbFRV652AbsGLW8n0ac7H2FlQ... .
Yes, create the new base with 4 timepoints. And rerun the long for each timepoint.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Eszter Boros Sent: Friday, January 17, 2025 1:00 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal analyses, more than 2 timepoints
External Email - Use Caution I apologize! I think I have just realized that I can create one base based on 4 time points, right?
recon-all -base <templateid> -tp <tp1id> -tp <tp2id> -tp <tp3id> -tp <tp4id> -all
Thank you!
Eszter Boros <boros.eszter0226@gmail.commailto:boros.eszter0226@gmail.com> ezt írta (időpont: 2025. jan. 17., P, 12:55): Thank you for the quick response! I appreciate it. I am not sure what you mean by rerun specifically. Should I rerun separate analyses for 0-6 months, 0-1year, and 0-1.5 years? Or can I analyze all of them in the same model? I do not think I should rerun 0-6months if that is already analyzed, right? Thank you!
Huang, Yujing <YHUANG43@mgh.harvard.edumailto:YHUANG43@mgh.harvard.edu> ezt írta (időpont: 2025. jan. 15., Sze, 16:20): Here is the tutorial for longitudinal processing - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessinghttps://secure-web.cisco.com/15H1lCCgBPzjRd89RtWHk9KzzXEM40qS4p5I4M8lLImOuILgk9B2URL3DUZcCGz6YEq5oacf5Nj2RpX0eQkDbqxV4PjEohumGH0gd3YamnnV5d-nLHWPquKo9tU8Uo7kq_umH14-6v9qKUmsJelShkrsI4WlFL8vRp5PjRNlcPS8ZOvYdesO-AqZgMyJmEtm_QOWDyJxZJCLz8DDdINaGy3rGaTjQTu5cknKbGlhOrxDO_75AymtC3xHgaloIN6C2cwaMu7qxR40P7dYtSmWlD42vFTV5u2mXCYBaxPmwjh-GpJuj8XLSASmlPcTOVm3FCDrZ7QuE6ou82H_-KwR6OA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalProcessing
The 'base' and 'long' steps of the longitudinal processing should be re-run after adding new timepoints.
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Eszter Boros Sent: Wednesday, January 15, 2025 1:52 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] longitudinal analyses, more than 2 timepoints
External Email - Use Caution Dear FreeSurfer Team,
We are analyzing some longitudinal data (baseline [0], 6 months, 1 year, 1.5 years) using FreeSurfer 7.4.1. We already analyzed two timepoints (basline[0] and 6 months) but now we are trying to look at 4 timepoints in total.
I was wondering what the best way would be to do this. For the longitudinal processing, should we create 3 bases/within-subject templates between 0-6 months (this is already done), 0-1year, 0-1.5years), or between 0-6months, 6months-1year, 1year-1.5years. Or both?
Also, is it okay to correct/edit only the bases?
After the longitudinal processing, can we create a Longitudinal Table and apply the two-stage model (LongitudinalTwoStageModel) method? Or because of the 4 time points, we need to apply something else.
Thank you for your help in advance!
All the best, Eszter _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1VnOtHaDxJ2OrtICt27VxI5KsyGvyE4zZcz2geKvcTAKUof6rO3vnrbF7KAgMEdSadh45yNODJkIx7QLyN5fM0URYq4ymEs4DR0wUG-QVEaxZ2cHHCdMOlEzWz_RtJPbRM2t27l4o2Mc8vbLGySyjSYDier4sjpneTwN5q_PK-U_NAtH9iQ5HQj9ZxkHdl_Yb5Vhf4nbUn7fS5pSA3WcOOOrPqRTfzf46dKXDiOLLiH6yBlnTOtakQZsojCRaU0DWAtzeOlozZ9bFVPrmyCLd74EdYE6u77c9HWYLW8X3MC8G6B0I2Tv1UERC8_W6S6fdxp76jxQjjgxNs8nw2Z-0PQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1onxNuFESdAX_xYJxmT4easbFRV652AbsGLW8n0ac7H2FlQlDtDNZXRLq0Xfcnwo3CxeYN0I-DV8OLqSEwrfez7i5rZXML8bI-F0iitXiA4t7Vg0jHGn0b76eB1BQLvwsLbP5Nm3xNOBEMynlqxrF8KsR3QZ3qbmelNpznRwIrcNugxcppF3_cOVgq7jRhCy6yWfPtwVD_7o4u7-MY6kvbSBeVEQDTcljugxcJU2rpfy_w2VgS8yDAtnj2yZsqlonJQ3hc5_02VEhDJ48MY0UWN5AKd0nA54RGm74-mi_eM_WOXnLVpJ0Vb8m0dcHURLGFSyA6SE57h2ptU796yU0ig/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1onxNuFESdAX_xYJxmT4easbFRV652AbsGLW8n0ac7H2FlQlDtDNZXRLq0Xfcnwo3CxeYN0I-DV8OLqSEwrfez7i5rZXML8bI-F0iitXiA4t7Vg0jHGn0b76eB1BQLvwsLbP5Nm3xNOBEMynlqxrF8KsR3QZ3qbmelNpznRwIrcNugxcppF3_cOVgq7jRhCy6yWfPtwVD_7o4u7-MY6kvbSBeVEQDTcljugxcJU2rpfy_w2VgS8yDAtnj2yZsqlonJQ3hc5_02VEhDJ48MY0UWN5AKd0nA54RGm74-mi_eM_WOXnLVpJ0Vb8m0dcHURLGFSyA6SE57h2ptU796yU0ig/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> .
you can use the two stage model
On 1/15/2025 1:52 PM, Eszter Boros wrote:
External Email - Use Caution
Dear FreeSurfer Team, We are analyzing some longitudinal data (baseline [0], 6 months, 1 year, 1.5 years) using FreeSurfer 7.4.1. We already analyzed two timepoints (basline[0] and 6 months) but now we are trying to look at 4 timepoints in total.
I was wondering what the best way would be to do this. For the longitudinal processing, should we create 3 bases/within-subject templates between 0-6 months (this is already done), 0-1year, 0-1.5years), or between 0-6months, 6months-1year, 1year-1.5years. Or both?
Also, is it okay to correct/edit only the bases?
After the longitudinal processing, can we create a Longitudinal Table and apply the two-stage model (LongitudinalTwoStageModel) method? Or because of the 4 time points, we need to apply something else.
Thank you for your help in advance!
All the best, Eszter
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Eszter Boros -
Huang, Yujing