External Email - Use Caution
Dear Freesurfer experts,
I am trying to do a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
Although I have run a paired t-test, now I would like to do a repeated measures anova 2x2, since I am doing the same analyses with other data in other softwares.
I am trying to follow the tutorial https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grF..., but I have several doubts when designing the FSGD file as well as the contrasts.
How should it be the FSGD file?
I have seen in a previous post the following design for the same number fo groups and time points:
GroupDescriptorFile 1
Class Subject1
Class Subject2
Variables Tp1vsTp2.GrExp Tp1vsTp2.GrControl
Input Subject1_time1 Subject1 1 0
Input Subject1_time2 Subject1 -1 0
Input Subject2_time1 Subject2 0 1
Input Subject2_time2 Subject02 0 -1
Design matrix:
1 0 1 0
1 0 -1 0
0 1 0 1
0 1 0 -1
Contrasts (.mtx files): Tp1vsTp2.GrExp 0 0 1 0 Tp1vsTp2.GrControl 0 0 0 -1 Interaction 0 0 1 -1
Would this design be the correct one to use in this case?
Alternatively, could it be this the correct one?
GroupDescriptorFile 1
Class Subject1
Class Subject2
Variables Tp1vsTp2 Groupxtime
Input Subject1_time1 Subject1 1 1
Input Subject1_time2 Subject1 -1 *-1*
Input Subject2_time1 Subject2 1 *-1*
Input Subject2_time2 Subject02 -1 1
Design matrix:
1 0 1 1
1 0 -1 -1
0 1 1 -1
0 1 -1 1
Contrasts (.mtx files):
Tp1vsTp2 0 0 1 0
Groupxtime Interaction 0 0 0 1
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
neurolab.deusto.es
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer your question, the first example you give is the right way to handle it.
On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote:
External Email - Use Caution
Dear Freesurfer experts,
I am trying to do a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
Although I have run a paired t-test, now I would like to do a repeated measures anova 2x2, since I am doing the same analyses with other data in other softwares.
I am trying to follow the tutorial *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-sr-c0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-MwCGM_OotAt9VM1mzmm1MUuXbYtZC4-QfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-3CdqLLZnJRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova, but I have several doubts when designing the FSGD file as well as the contrasts.
How should it be the FSGD file?
I have seen in a previous post the following design for the same number fo groups and time points:
GroupDescriptorFile 1
Class Subject1
Class Subject2
Variables Tp1vsTp2.GrExp Tp1vsTp2.GrControl
Input Subject1_time1 Subject1 1 0
Input Subject1_time2 Subject1 -1 0
Input Subject2_time1 Subject2 0 1
Input Subject2_time2 Subject02 0 -1
Design matrix:
1 0 1 0
1 0 -1 0
0 1 0 1
0 1 0 -1
Contrasts (.mtx files): Tp1vsTp2.GrExp 0 0 1 0 Tp1vsTp2.GrControl 0 0 0 -1 Interaction 0 0 1 -1
Would this design be the correct one to use in this case?
Alternatively, could it be this the correct one?
GroupDescriptorFile 1
Class Subject1
Class Subject2
Variables Tp1vsTp2 Groupxtime
Input Subject1_time1 Subject1 1 1
Input Subject1_time2 Subject1 -1 *-1*
Input Subject2_time1 Subject2 1 *-1*
Input Subject2_time2 Subject02 -1 1
Design matrix:
1 0 1 1
1 0 -1 -1
0 1 1 -1
0 1 -1 1
Contrasts (.mtx files):
Tp1vsTp2 0 0 1 0
Groupxtime Interaction 0 0 0 1
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Douglas,
Thank you very much for your rapid response. I have another question.
I am following the FS Repeated Measures tutorial and therefore, I ran this: mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rmanova.fsgd. However, in the FS Group Analysis tutorial, it says that you must include "--cache-in thickness.fwhm10.fsaverage" if the data was preprocessed with recon-all with the -qcache option, which was my case. As I am doing longitudinal analyses, do I have to skip this option and just follow the Repeated Measures tutorial or do I have to include the --cache option?
Thank you very much. Best regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
neurolab.deusto.es
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El jue., 5 nov. 2020 a las 15:58, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer your question, the first example you give is the right way to handle it.
On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Freesurfer experts,
I am trying to do a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
Although I have run a paired t-test, now I would like to do a repeated measures anova 2x2, since I am doing the same analyses with other data in other softwares.
I am trying to follow the tutorial *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/11u6-IyY2-P7w7M4zmGiLCyaG6g2vViEpx4ag8H474t_vAc... https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-sr-c0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-MwCGM_OotAt9VM1mzmm1MUuXbYtZC4-QfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-3CdqLLZnJRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova, but I have several doubts when designing the FSGD file as well as the contrasts.
How should it be the FSGD file?
I have seen in a previous post the following design for the same number fo groups and time points:
GroupDescriptorFile 1
Class Subject1
Class Subject2
Variables Tp1vsTp2.GrExp Tp1vsTp2.GrControl
Input Subject1_time1 Subject1 1 0
Input Subject1_time2 Subject1 -1 0
Input Subject2_time1 Subject2 0 1
Input Subject2_time2 Subject02 0 -1
Design matrix:
1 0 1 0
1 0 -1 0
0 1 0 1
0 1 0 -1
Contrasts (.mtx files): Tp1vsTp2.GrExp 0 0 1 0 Tp1vsTp2.GrControl 0 0 0 -1 Interaction 0 0 1 -1
Would this design be the correct one to use in this case?
Alternatively, could it be this the correct one?
GroupDescriptorFile 1
Class Subject1
Class Subject2
Variables Tp1vsTp2 Groupxtime
Input Subject1_time1 Subject1 1 1
Input Subject1_time2 Subject1 -1 *-1*
Input Subject2_time1 Subject2 1 *-1*
Input Subject2_time2 Subject02 -1 1
Design matrix:
1 0 1 1
1 0 -1 -1
0 1 1 -1
0 1 -1 1
Contrasts (.mtx files):
Tp1vsTp2 0 0 1 0
Groupxtime Interaction 0 0 0 1
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Jem34chpPCHsjtBsJuqJZVyROTvpLIYYdJJC55-ICnVW3E...
Oh, that's an error, you do not have to include --cache-in. Where is that page?
On 11/5/2020 10:32 AM, Agurne Sampedro Calvete wrote:
External Email - Use Caution
Dear Douglas,
Thank you very much for your rapid response. I have another question.
I am following the FS Repeated Measures tutorial and therefore, I ran this: mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rmanova.fsgd. However, in the FS Group Analysis tutorial, it says that you must include "--cache-in thickness.fwhm10.fsaverage" if the data was preprocessed with recon-all with the -qcache option, which was my case. As I am doing longitudinal analyses, do I have to skip this option and just follow the Repeated Measures tutorial or do I have to include the --cache option?
Thank you very much. Best regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El jue., 5 nov. 2020 a las 15:58, Douglas N. Greve (<dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>) escribió:
In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer your question, the first example you give is the right way to handle it. On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote:External Email - Use Caution Dear Freesurfer experts, I am trying to do a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment). Although I have run a paired t-test, now I would like to do a repeated measures anova 2x2, since I am doing the same analyses with other data in other softwares. I am trying to follow the tutorial *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova <https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-sr-c0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-MwCGM_OotAt9VM1mzmm1MUuXbYtZC4-QfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-3CdqLLZnJRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova>, but I have several doubts when designing the FSGD file as well as the contrasts. How should it be the FSGD file? I have seen in a previous post the following design for the same number fo groups and time points: GroupDescriptorFile 1 Class Subject1 Class Subject2 Variables Tp1vsTp2.GrExp Tp1vsTp2.GrControl Input Subject1_time1 Subject1 1 0 Input Subject1_time2 Subject1 -1 0 Input Subject2_time1 Subject2 0 1 Input Subject2_time2 Subject02 0 -1 Design matrix: 1 0 1 0 1 0 -1 0 0 1 0 1 0 1 0 -1 Contrasts (.mtx files): Tp1vsTp2.GrExp 0 0 1 0 Tp1vsTp2.GrControl 0 0 0 -1 Interaction 0 0 1 -1 Would this design be the correct one to use in this case? Alternatively, could it be this the correct one? GroupDescriptorFile 1 Class Subject1 Class Subject2 Variables Tp1vsTp2 Groupxtime Input Subject1_time1 Subject1 1 1 Input Subject1_time2 Subject1 -1 *-1* Input Subject2_time1 Subject2 1 *-1* Input Subject2_time2 Subject02 -1 1 Design matrix: 1 0 1 1 1 0 -1 -1 0 1 1 -1 0 1 -1 1 Contrasts (.mtx files): Tp1vsTp2 0 0 1 0 Groupxtime Interaction 0 0 0 1 Thank you very much in advance. Kind regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es <http://secure-web.cisco.com/1J2XHqATjb-s81WNLHHOzFHoMov247ukeyY9r_63MCuIYY3b3cgBooSYVXAHcxmruuUhAJRQeOK_M6GhmpQ2HLsoPViHsaOnuQmnS_hX44VhcAXEpVQmkpDhtamFGdp_Y3WSVnP0Hb0VMfltJoov6c0TVAyZfGD7j4wcdLUcORgyyH2uu_WSTkVwMZ87NUx0paSiYbguuSG9LFBN_NCd9ZQ/http%3A%2F%2Fneurolab.deusto.es%2F> Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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/freesurfer <https://secure-web.cisco.com/1Jem34chpPCHsjtBsJuqJZVyROTvpLIYYdJJC55-ICnVW3ESEKCmsC6eW9LB5d5ifNKvbDn5kjCTLUgekR_iPR1nUUewDdNSAar__UZ9NH2kcFsqXd4ArR4JKSJL6XT6lbPeqIve9m1qOwslfkpsChNtyAeWFsRGhX-oH5GTyh0j92WiaYNTiqROCWdLU6aRLwzbA0WJf6RWmMJFXv5cB4Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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/freesurfer <https://secure-web.cisco.com/1Jem34chpPCHsjtBsJuqJZVyROTvpLIYYdJJC55-ICnVW3ESEKCmsC6eW9LB5d5ifNKvbDn5kjCTLUgekR_iPR1nUUewDdNSAar__UZ9NH2kcFsqXd4ArR4JKSJL6XT6lbPeqIve9m1qOwslfkpsChNtyAeWFsRGhX-oH5GTyh0j92WiaYNTiqROCWdLU6aRLwzbA0WJf6RWmMJFXv5cB4Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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I found it here: https://secure-web.cisco.com/1Pobz-1CRgeaN25ufKu4UcOwbvjX2LjQiAacXtHLnJRq3FQ...
I may have misunderstood.
Thank you very much.
Regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
neurolab.deusto.es
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El vie., 6 nov. 2020 a las 15:57, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:
Oh, that's an error, you do not have to include --cache-in. Where is that page?
On 11/5/2020 10:32 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Douglas,
Thank you very much for your rapid response. I have another question.
I am following the FS Repeated Measures tutorial and therefore, I ran this: mris_preproc --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh --fsgd rmanova.fsgd. However, in the FS Group Analysis tutorial, it says that you must include "--cache-in thickness.fwhm10.fsaverage" if the data was preprocessed with recon-all with the -qcache option, which was my case. As I am doing longitudinal analyses, do I have to skip this option and just follow the Repeated Measures tutorial or do I have to include the --cache option?
Thank you very much. Best regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
El jue., 5 nov. 2020 a las 15:58, Douglas N. Greve (< dgreve@mgh.harvard.edu>) escribió:
In this case, the paired-t is identical to RM 2x2 ANOVA. But to answer your question, the first example you give is the right way to handle it.
On 11/5/2020 4:32 AM, Agurne Sampedro Calvete wrote:
External Email - Use CautionDear Freesurfer experts,
I am trying to do a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment).
Although I have run a paired t-test, now I would like to do a repeated measures anova 2x2, since I am doing the same analyses with other data in other softwares.
I am trying to follow the tutorial *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wVu5Gz4iksiDQpw3WC4tPugyfo6UlKc1Cl2Uk8w-z5ecya... https://secure-web.cisco.com/1xcEvqAuPN3MsqK1JjC6qoZbooZS3kpB4WEU1Lx8hK28grFkOWFgj7ja5TXppcZRh8Vr2s3TJyQKT-sr-c0qt4XJSU7f74cElgVAI4K1nOBI5i5L0YQBzYutTVn-MwCGM_OotAt9VM1mzmm1MUuXbYtZC4-QfIujBH30LAwD5RtwZ6vGRv4JC7ocISixV0s52BsCadrLE2J-3CdqLLZnJRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova, but I have several doubts when designing the FSGD file as well as the contrasts.
How should it be the FSGD file?
I have seen in a previous post the following design for the same number fo groups and time points:
GroupDescriptorFile 1
Class Subject1
Class Subject2
Variables Tp1vsTp2.GrExp Tp1vsTp2.GrControl
Input Subject1_time1 Subject1 1 0
Input Subject1_time2 Subject1 -1 0
Input Subject2_time1 Subject2 0 1
Input Subject2_time2 Subject02 0 -1
Design matrix:
1 0 1 0
1 0 -1 0
0 1 0 1
0 1 0 -1
Contrasts (.mtx files): Tp1vsTp2.GrExp 0 0 1 0 Tp1vsTp2.GrControl 0 0 0 -1 Interaction 0 0 1 -1
Would this design be the correct one to use in this case?
Alternatively, could it be this the correct one?
GroupDescriptorFile 1
Class Subject1
Class Subject2
Variables Tp1vsTp2 Groupxtime
Input Subject1_time1 Subject1 1 1
Input Subject1_time2 Subject1 -1 *-1*
Input Subject2_time1 Subject2 1 *-1*
Input Subject2_time2 Subject02 -1 1
Design matrix:
1 0 1 1
1 0 -1 -1
0 1 1 -1
0 1 -1 1
Contrasts (.mtx files):
Tp1vsTp2 0 0 1 0
Groupxtime Interaction 0 0 0 1
Thank you very much in advance.
Kind regards,
Agurne
Neuropsychology of Severe Medical Conditions Research Team
Dpt of Methods and Experimental Psychology Faculty of Psychology and Education
University of Deusto
Avda. de las Universidades 24,
48007, Bilbao (Spain)
Phone: +34 944139000 (ext. 3015)
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1iykrgjwvbDcClUYDaw_oK-rq-rQXVdASuQVs9xf8vSdozu... https://secure-web.cisco.com/1Jem34chpPCHsjtBsJuqJZVyROTvpLIYYdJJC55-ICnVW3ESEKCmsC6eW9LB5d5ifNKvbDn5kjCTLUgekR_iPR1nUUewDdNSAar__UZ9NH2kcFsqXd4ArR4JKSJL6XT6lbPeqIve9m1qOwslfkpsChNtyAeWFsRGhX-oH5GTyh0j92WiaYNTiqROCWdLU6aRLwzbA0WJf6RWmMJFXv5cB4Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Agurne Sampedro Calvete -
Douglas N. Greve