External Email - Use Caution
Dear FreeSurfer Team,
We are trying to run some longitudinal data using FreeSurfer 7.4.1. We have one group and 3 scans. We would like to see the changes between these timepoints. I am not sure how to proceed with the GLM because I found two tutorials.
One here is saying I should create a longitudinal qdec table including fsid-base column and years/timepoints then run mri_glmfit --osgm https://secure-web.cisco.com/12qS0acHTgwXhZDIytchwCnsXkPJ57shyJ2uQEuf0WkwB9m...
The other one is saying to do a paired analysis. This one does not include the base and years data. https://secure-web.cisco.com/1voT6D0EOLTXJrVgGSmPK-onn8JIxg74dwxqLG9An8DuChO...
How should I proceed? Thank you!
Best regards, Eszter
The first one is a more complicated model that includes a mixed effects design. Harder to set up. The second is a paired ttest; this is simple and good if you only have two time points. For three time points I would use https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
On 2/13/2026 1:22 PM, Eszter Boros wrote:
External Email - Use Caution
Dear FreeSurfer Team,
We are trying to run some longitudinal data using FreeSurfer 7.4.1. We have one group and 3 scans. We would like to see the changes between these timepoints. I am not sure how to proceed with the GLM because I found two tutorials.
One here is saying I should create a longitudinal qdec table including fsid-base column and years/timepoints then run mri_glmfit --osgm https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel https://secure-web.cisco.com/12qS0acHTgwXhZDIytchwCnsXkPJ57shyJ2uQEuf0WkwB9mHKD_F025ScXa3x_w6UTTa033qwm9kh39bvL8QtSvm8CzIADZLkiusS96akb1z7Siecnj7s395hVQx4WyNGElMWwb5UKSw3mj-CbSpGMOKq3YCyjB9ujY2NWo0MWY1Vhhq37r9GIi0_ozz0pFf6kISjrCpP2gtQ4TraV2331sVFRPyTvzn4MrLoSitQycAeOPXH9hHu8ZnMwgdRSeIExNfOYfuHghbnsJJq87iJb0iR7b1qKZO_NbkvTRmuxKJL3coCXnVN9HVgiWtgh7U8lO6tJwVADL19Th516PqsyQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalTwoStageModel
The other one is saying to do a paired analysis. This one does not include the base and years data. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis https://secure-web.cisco.com/1voT6D0EOLTXJrVgGSmPK-onn8JIxg74dwxqLG9An8DuChONQTsGe_Ofrr8nuwU-pri3bChh8YFXTyJ9ZinYiCLKxWXtDm2HnFq-Z9QFa0hy8KhVjsDJ5vAtZWGokRHhPQD_rDPKdYl1iAbMIIAtei1aXlzfgpfB5x61LVSxzxTMT_9qREac9pwiqNLZ7c1H_bCt-iJlBnAqBR9BXIOAbpHKJWzarwCGRO9ys1uXBGar4DfjHmoSBozw1WA8mud3SeKpgobTnFDkAA9MK2rQn8nk0V703KLn6BKSkpTNKRMmeFeneh_h0HcLXp4cAjLtzZjsqqlGJLtQSBpWXKFowOA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis
How should I proceed? Thank you!
Best regards, Eszter
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Thank you for the prompt reply! Should I spatially smooth as part of the RepeatedMeasuresAnova? I saw that it is optional. But I wonder why. I already used -qcach as part of recon-all. So I do not need anything from this script and I can skip it, right? mri_surf2surf --s fsaverage --hemi lh --fwhm 5\ --sval lh.thickness.mgh \ --tval lh.thickness.sm05.mgh
Also, we were considering LME in Matlab as well before reading your response about RepeatedMeasuresAnova. Do you think that is "good enough" for publication purposes? Or LME is the preferred method.
Thank you!
Best regards, Eszter
Douglas N. Greve dgreve@mgh.harvard.edu ezt írta (időpont: 2026. febr. 13., P, 17:58):
The first one is a more complicated model that includes a mixed effects design. Harder to set up. The second is a paired ttest; this is simple and good if you only have two time points. For three time points I would use https://secure-web.cisco.com/12ccT5h9BKgzrD8dFXt3AiTFrqb2_FMNi0EcWnFk1kUDJwt...
On 2/13/2026 1:22 PM, Eszter Boros wrote:
External Email - Use CautionDear FreeSurfer Team,
We are trying to run some longitudinal data using FreeSurfer 7.4.1. We have one group and 3 scans. We would like to see the changes between these timepoints. I am not sure how to proceed with the GLM because I found two tutorials.
One here is saying I should create a longitudinal qdec table including fsid-base column and years/timepoints then run mri_glmfit --osgm https://secure-web.cisco.com/1rEpYusYBbceA5sTNnwjaKH4bZ1nXw3Gbxs_J7Z4gS3KdjN... https://secure-web.cisco.com/12qS0acHTgwXhZDIytchwCnsXkPJ57shyJ2uQEuf0WkwB9mHKD_F025ScXa3x_w6UTTa033qwm9kh39bvL8QtSvm8CzIADZLkiusS96akb1z7Siecnj7s395hVQx4WyNGElMWwb5UKSw3mj-CbSpGMOKq3YCyjB9ujY2NWo0MWY1Vhhq37r9GIi0_ozz0pFf6kISjrCpP2gtQ4TraV2331sVFRPyTvzn4MrLoSitQycAeOPXH9hHu8ZnMwgdRSeIExNfOYfuHghbnsJJq87iJb0iR7b1qKZO_NbkvTRmuxKJL3coCXnVN9HVgiWtgh7U8lO6tJwVADL19Th516PqsyQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalTwoStageModel
The other one is saying to do a paired analysis. This one does not include the base and years data. https://secure-web.cisco.com/1Gtu6seX2gXf2IHDWnpVlrRycqNmi-9W5qLhD7WnbBO92Hx... https://secure-web.cisco.com/1voT6D0EOLTXJrVgGSmPK-onn8JIxg74dwxqLG9An8DuChONQTsGe_Ofrr8nuwU-pri3bChh8YFXTyJ9ZinYiCLKxWXtDm2HnFq-Z9QFa0hy8KhVjsDJ5vAtZWGokRHhPQD_rDPKdYl1iAbMIIAtei1aXlzfgpfB5x61LVSxzxTMT_9qREac9pwiqNLZ7c1H_bCt-iJlBnAqBR9BXIOAbpHKJWzarwCGRO9ys1uXBGar4DfjHmoSBozw1WA8mud3SeKpgobTnFDkAA9MK2rQn8nk0V703KLn6BKSkpTNKRMmeFeneh_h0HcLXp4cAjLtzZjsqqlGJLtQSBpWXKFowOA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis
How should I proceed? Thank you!
Best regards, Eszter
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https://secure-web.cisco.com/18LEWis-xAx-H8zDiJUWI6K-Zxe-V3SNk6nqvYje3-9Hohj... 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/1a4RdtzIU8rKJ16kkq9qQRK_TJbGVENXogd-zhRJ1jbxcmf... < https://secure-web.cisco.com/1a4RdtzIU8rKJ16kkq9qQRK_TJbGVENXogd-zhRJ1jbxcmf... .
smoothing decisions won't rely on whether the analysis is an rm-anova or something else. how much to smooth depends on a lot of things, eg, the spatial structure of your contrast of interest
On 2/19/2026 3:06 PM, Eszter Boros wrote:
External Email - Use Caution
Thank you for the prompt reply! Should I spatially smooth as part of the RepeatedMeasuresAnova? I saw that it is optional. But I wonder why. I already used -qcach as part of recon-all. So I do not need anything from this script and I can skip it, right? mri_surf2surf --s fsaverage --hemi lh --fwhm 5\ --sval lh.thickness.mgh \ --tval lh.thickness.sm05.mgh
Also, we were considering LME in Matlab as well before reading your response about RepeatedMeasuresAnova. Do you think that is "good enough" for publication purposes? Or LME is the preferred method.
Thank you!
Best regards, Eszter
Douglas N. Greve dgreve@mgh.harvard.edu ezt írta (időpont: 2026. febr. 13., P, 17:58):
The first one is a more complicated model that includes a mixed effects design. Harder to set up. The second is a paired ttest; this is simple and good if you only have two time points. For three time points I would use https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova <https://secure-web.cisco.com/12ccT5h9BKgzrD8dFXt3AiTFrqb2_FMNi0EcWnFk1kUDJwt58qkgX_cSM-CKgX2HPxGJZoUjhTSgVQ25rZYiRmPJlrHXPUU18RPKGjosaivQlp8XdiVSebTpmyVQtV_bIYBw5faa2IYMawhmoVjP5wSYnwjTibBRJnr0C6hwuVzCxPxnEvImtHClavVtaWrIH3Vq0HT-HyVLNefLkWxS7681VNRR5ELYsUHIbDzEUxFo9LtNKCo9KXUrYHZ8CJpEwCmjLo5QxtiPxcS-ZEKAxVY0gs3BkHlK5FkK1p08OueUAXQNwg8p2EzDLfenB9iFT/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova> On 2/13/2026 1:22 PM, Eszter Boros wrote:External Email - Use Caution Dear FreeSurfer Team, We are trying to run some longitudinal data using FreeSurfer 7.4.1. We have one group and 3 scans. We would like to see the changes between these timepoints. I am not sure how to proceed with the GLM because I found two tutorials. One here is saying I should create a longitudinal qdec table including fsid-base column and years/timepoints then run mri_glmfit --osgm https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel <https://secure-web.cisco.com/12qS0acHTgwXhZDIytchwCnsXkPJ57shyJ2uQEuf0WkwB9mHKD_F025ScXa3x_w6UTTa033qwm9kh39bvL8QtSvm8CzIADZLkiusS96akb1z7Siecnj7s395hVQx4WyNGElMWwb5UKSw3mj-CbSpGMOKq3YCyjB9ujY2NWo0MWY1Vhhq37r9GIi0_ozz0pFf6kISjrCpP2gtQ4TraV2331sVFRPyTvzn4MrLoSitQycAeOPXH9hHu8ZnMwgdRSeIExNfOYfuHghbnsJJq87iJb0iR7b1qKZO_NbkvTRmuxKJL3coCXnVN9HVgiWtgh7U8lO6tJwVADL19Th516PqsyQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalTwoStageModel> The other one is saying to do a paired analysis. This one does not include the base and years data. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis <https://secure-web.cisco.com/1voT6D0EOLTXJrVgGSmPK-onn8JIxg74dwxqLG9An8DuChONQTsGe_Ofrr8nuwU-pri3bChh8YFXTyJ9ZinYiCLKxWXtDm2HnFq-Z9QFa0hy8KhVjsDJ5vAtZWGokRHhPQD_rDPKdYl1iAbMIIAtei1aXlzfgpfB5x61LVSxzxTMT_9qREac9pwiqNLZ7c1H_bCt-iJlBnAqBR9BXIOAbpHKJWzarwCGRO9ys1uXBGar4DfjHmoSBozw1WA8mud3SeKpgobTnFDkAA9MK2rQn8nk0V703KLn6BKSkpTNKRMmeFeneh_h0HcLXp4cAjLtzZjsqqlGJLtQSBpWXKFowOA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis> How should I proceed? Thank you! Best regards, Eszter _______________________________________________ Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ <https://secure-web.cisco.com/18LEWis-xAx-H8zDiJUWI6K-Zxe-V3SNk6nqvYje3-9Hohjt6CDUhR27d_8m8TwqjTT4CfHKJnRcEftYCemIib3hAT9c4pR1TGReYLaBaXGTLyc94RjlPF96tRpvIyANA6E2cclm9e9SfrhSdc4E7ll6Ga9zcfuPc2CHQshMBtWd5-5fIRSChMFDSf-aMZl-x8AFbjZ1YxdZ-s9QcXv-5Q1Gkv-tlBKbiepUGPBlwlq1XcuA36xSjBJRwwX44JchxSnIL8YUtiQ9LvYvbd5HJz5EvhiPnNW_R4-1t9xUmzBmx_n3UlZkgOyz-tKD78-I3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F>_______________________________________________ Freesurfer mailing list -- freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ <https://secure-web.cisco.com/18LEWis-xAx-H8zDiJUWI6K-Zxe-V3SNk6nqvYje3-9Hohjt6CDUhR27d_8m8TwqjTT4CfHKJnRcEftYCemIib3hAT9c4pR1TGReYLaBaXGTLyc94RjlPF96tRpvIyANA6E2cclm9e9SfrhSdc4E7ll6Ga9zcfuPc2CHQshMBtWd5-5fIRSChMFDSf-aMZl-x8AFbjZ1YxdZ-s9QcXv-5Q1Gkv-tlBKbiepUGPBlwlq1XcuA36xSjBJRwwX44JchxSnIL8YUtiQ9LvYvbd5HJz5EvhiPnNW_R4-1t9xUmzBmx_n3UlZkgOyz-tKD78-I3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F> 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://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1a4RdtzIU8rKJ16kkq9qQRK_TJbGVENXogd-zhRJ1jbxcmflvG2KFQA_52uV4HPwxa23buB7kkJRIvSQqHh3PCRaab9SguH_XwiP0sbeTE56OWFFkGPSxIHQejpsNNFM1tYmshkPqL4oOFCYdrQb82Wk3Lqb13jOl8N3ODBx7OPHIBxIOEpNWBPY8_mPfzWamJ8O4VsX-wAPUDxVf5NAZOtj-NM4eS1imb28Rt68I7AavPUKbQJo03y1b_SOs42hx97sE5JpZcFr5LDNcrtrkzknt9dAP4C7Tz49tFjTZWjU7n-LMEiVbYEIVPIw2w_NC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> <https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1a4RdtzIU8rKJ16kkq9qQRK_TJbGVENXogd-zhRJ1jbxcmflvG2KFQA_52uV4HPwxa23buB7kkJRIvSQqHh3PCRaab9SguH_XwiP0sbeTE56OWFFkGPSxIHQejpsNNFM1tYmshkPqL4oOFCYdrQb82Wk3Lqb13jOl8N3ODBx7OPHIBxIOEpNWBPY8_mPfzWamJ8O4VsX-wAPUDxVf5NAZOtj-NM4eS1imb28Rt68I7AavPUKbQJo03y1b_SOs42hx97sE5JpZcFr5LDNcrtrkzknt9dAP4C7Tz49tFjTZWjU7n-LMEiVbYEIVPIw2w_NC/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> .
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Thank you! We already smoothed the data with -qcash, so we will skip this step. Would rm-anova work for publication purposes? Or just for exploration, and LME in Matlab would be the preferred method.
Thank you!
Best regards, Eszter
Douglas N. Greve dgreve@mgh.harvard.edu ezt írta (időpont: 2026. febr. 23., H, 22:07):
smoothing decisions won't rely on whether the analysis is an rm-anova or something else. how much to smooth depends on a lot of things, eg, the spatial structure of your contrast of interest
On 2/19/2026 3:06 PM, Eszter Boros wrote:
External Email - Use CautionThank you for the prompt reply! Should I spatially smooth as part of the RepeatedMeasuresAnova? I saw that it is optional. But I wonder why. I already used -qcach as part of recon-all. So I do not need anything from this script and I can skip it, right? mri_surf2surf --s fsaverage --hemi lh --fwhm 5\ --sval lh.thickness.mgh \ --tval lh.thickness.sm05.mgh
Also, we were considering LME in Matlab as well before reading your response about RepeatedMeasuresAnova. Do you think that is "good enough" for publication purposes? Or LME is the preferred method.
Thank you!
Best regards, Eszter
Douglas N. Greve dgreve@mgh.harvard.edu ezt írta (időpont: 2026. febr. 13., P, 17:58):
The first one is a more complicated model that includes a mixed effects design. Harder to set up. The second is a paired ttest; this is simple and good if you only have two time points. For three time points I would use https://secure-web.cisco.com/1G2OehDl5ma9ciFpB1dGlKQpTv_iJhw1uHlFrJ9hU_2DGXu... https://secure-web.cisco.com/12ccT5h9BKgzrD8dFXt3AiTFrqb2_FMNi0EcWnFk1kUDJwt58qkgX_cSM-CKgX2HPxGJZoUjhTSgVQ25rZYiRmPJlrHXPUU18RPKGjosaivQlp8XdiVSebTpmyVQtV_bIYBw5faa2IYMawhmoVjP5wSYnwjTibBRJnr0C6hwuVzCxPxnEvImtHClavVtaWrIH3Vq0HT-HyVLNefLkWxS7681VNRR5ELYsUHIbDzEUxFo9LtNKCo9KXUrYHZ8CJpEwCmjLo5QxtiPxcS-ZEKAxVY0gs3BkHlK5FkK1p08OueUAXQNwg8p2EzDLfenB9iFT/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova
On 2/13/2026 1:22 PM, Eszter Boros wrote:
External Email - Use CautionDear FreeSurfer Team,
We are trying to run some longitudinal data using FreeSurfer 7.4.1. We have one group and 3 scans. We would like to see the changes between these timepoints. I am not sure how to proceed with the GLM because I found two tutorials.
One here is saying I should create a longitudinal qdec table including fsid-base column and years/timepoints then run mri_glmfit --osgm https://secure-web.cisco.com/1TMbsHEQqiiqN-4pMHmSuL5dx7axti0JVObMdgL5n587UHN... https://secure-web.cisco.com/12qS0acHTgwXhZDIytchwCnsXkPJ57shyJ2uQEuf0WkwB9mHKD_F025ScXa3x_w6UTTa033qwm9kh39bvL8QtSvm8CzIADZLkiusS96akb1z7Siecnj7s395hVQx4WyNGElMWwb5UKSw3mj-CbSpGMOKq3YCyjB9ujY2NWo0MWY1Vhhq37r9GIi0_ozz0pFf6kISjrCpP2gtQ4TraV2331sVFRPyTvzn4MrLoSitQycAeOPXH9hHu8ZnMwgdRSeIExNfOYfuHghbnsJJq87iJb0iR7b1qKZO_NbkvTRmuxKJL3coCXnVN9HVgiWtgh7U8lO6tJwVADL19Th516PqsyQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalTwoStageModel
The other one is saying to do a paired analysis. This one does not include the base and years data. https://secure-web.cisco.com/1Zu-NKZlYM_yAoWiNMukaTnorPBBbwBFVZsTXR1PfLw3avx... https://secure-web.cisco.com/1voT6D0EOLTXJrVgGSmPK-onn8JIxg74dwxqLG9An8DuChONQTsGe_Ofrr8nuwU-pri3bChh8YFXTyJ9ZinYiCLKxWXtDm2HnFq-Z9QFa0hy8KhVjsDJ5vAtZWGokRHhPQD_rDPKdYl1iAbMIIAtei1aXlzfgpfB5x61LVSxzxTMT_9qREac9pwiqNLZ7c1H_bCt-iJlBnAqBR9BXIOAbpHKJWzarwCGRO9ys1uXBGar4DfjHmoSBozw1WA8mud3SeKpgobTnFDkAA9MK2rQn8nk0V703KLn6BKSkpTNKRMmeFeneh_h0HcLXp4cAjLtzZjsqqlGJLtQSBpWXKFowOA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis
How should I proceed? Thank you!
Best regards, Eszter
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Hi Eszter,
I would always prefer LME , because it is more flexible (e.g. different spacing between time points, fixed vs random effects, easy to look at interactions etc). But not sure for your case, as we have no idea about what you even try to analyse with one group. Also we are not statisticians, which would be the right people to ask these questions.
There is also LME in R if you don’t want to pay Matlab fees, or in python.
Best, Martin
On 24. Feb 2026, at 21:41, Eszter Boros boros.eszter0226@gmail.com wrote: Thank you! We already smoothed the data with -qcash, so we will skip this step. Would rm-anova work for publication purposes? Or just for exploration, and LME in Matlab would be the preferred method.
Thank you!
Best regards, Eszter
Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> ezt írta (időpont: 2026. febr. 23., H, 22:07): smoothing decisions won't rely on whether the analysis is an rm-anova or something else. how much to smooth depends on a lot of things, eg, the spatial structure of your contrast of interest
On 2/19/2026 3:06 PM, Eszter Boros wrote:
Thank you for the prompt reply! Should I spatially smooth as part of the RepeatedMeasuresAnova? I saw that it is optional. But I wonder why. I already used -qcach as part of recon-all. So I do not need anything from this script and I can skip it, right? mri_surf2surf --s fsaverage --hemi lh --fwhm 5\ --sval lh.thickness.mgh \ --tval lh.thickness.sm05.mgh
Also, we were considering LME in Matlab as well before reading your response about RepeatedMeasuresAnova. Do you think that is "good enough" for publication purposes? Or LME is the preferred method.
Thank you!
Best regards, Eszter
Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> ezt írta (időpont: 2026. febr. 13., P, 17:58): The first one is a more complicated model that includes a mixed effects design. Harder to set up. The second is a paired ttest; this is simple and good if you only have two time points. For three time points I would use https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnovahttps://secure-web.cisco.com/12ccT5h9BKgzrD8dFXt3AiTFrqb2_FMNi0EcWnFk1kUDJwt58qkgX_cSM-CKgX2HPxGJZoUjhTSgVQ25rZYiRmPJlrHXPUU18RPKGjosaivQlp8XdiVSebTpmyVQtV_bIYBw5faa2IYMawhmoVjP5wSYnwjTibBRJnr0C6hwuVzCxPxnEvImtHClavVtaWrIH3Vq0HT-HyVLNefLkWxS7681VNRR5ELYsUHIbDzEUxFo9LtNKCo9KXUrYHZ8CJpEwCmjLo5QxtiPxcS-ZEKAxVY0gs3BkHlK5FkK1p08OueUAXQNwg8p2EzDLfenB9iFT/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova
On 2/13/2026 1:22 PM, Eszter Boros wrote:
External Email - Use Caution
Dear FreeSurfer Team,
We are trying to run some longitudinal data using FreeSurfer 7.4.1. We have one group and 3 scans. We would like to see the changes between these timepoints. I am not sure how to proceed with the GLM because I found two tutorials.
One here is saying I should create a longitudinal qdec table including fsid-base column and years/timepoints then run mri_glmfit --osgm https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModelhttps://secure-web.cisco.com/12qS0acHTgwXhZDIytchwCnsXkPJ57shyJ2uQEuf0WkwB9mHKD_F025ScXa3x_w6UTTa033qwm9kh39bvL8QtSvm8CzIADZLkiusS96akb1z7Siecnj7s395hVQx4WyNGElMWwb5UKSw3mj-CbSpGMOKq3YCyjB9ujY2NWo0MWY1Vhhq37r9GIi0_ozz0pFf6kISjrCpP2gtQ4TraV2331sVFRPyTvzn4MrLoSitQycAeOPXH9hHu8ZnMwgdRSeIExNfOYfuHghbnsJJq87iJb0iR7b1qKZO_NbkvTRmuxKJL3coCXnVN9HVgiWtgh7U8lO6tJwVADL19Th516PqsyQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLongitudinalTwoStageModel
The other one is saying to do a paired analysis. This one does not include the base and years data. https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysishttps://secure-web.cisco.com/1voT6D0EOLTXJrVgGSmPK-onn8JIxg74dwxqLG9An8DuChONQTsGe_Ofrr8nuwU-pri3bChh8YFXTyJ9ZinYiCLKxWXtDm2HnFq-Z9QFa0hy8KhVjsDJ5vAtZWGokRHhPQD_rDPKdYl1iAbMIIAtei1aXlzfgpfB5x61LVSxzxTMT_9qREac9pwiqNLZ7c1H_bCt-iJlBnAqBR9BXIOAbpHKJWzarwCGRO9ys1uXBGar4DfjHmoSBozw1WA8mud3SeKpgobTnFDkAA9MK2rQn8nk0V703KLn6BKSkpTNKRMmeFeneh_h0HcLXp4cAjLtzZjsqqlGJLtQSBpWXKFowOA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis
How should I proceed? Thank you!
Best regards, Eszter
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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Eszter Boros -
Reuter, Martin,Ph.D.