External Email - Use Caution Good morning Doug,
I am trying to create a contrast matrix (also attached as a text file) for the following conditions - I have two treatment arms A and B For treatment arm A, I have subjects 1, 2, 3 imaged at TP1, TP2, TP3 For treatment arm B, I have subjects 4, 5, 6 imaged at TP1, TP2, TP3. I have used the repeated measures ANOVA tutorial to set up some of the contrasts as follows - GroupDescriptorFile 1 Title A-Vs-B-Long Class A-TP1 Class B-TP1 Class A-TP2 Class B-TP2 Class A-TP3 Class B-TP3 Variables A-TP1-vs-A-TP2 A-TP1-vs-A-TP3 B-TP1-vs-B-TP2 B-TP1-vs-B-TP3 A-TP1-vs-B-TP1 A-TP2-vs-B-TP2 A-TP3-vs-B-TP3 Input sub1-TP1 A-TP1 1 1 0 0 Input sub2-TP1 A-TP1 1 1 0 0 Input sub3-TP1 A-TP1 1 1 0 0 Input sub4-TP1 B-TP1 0 0 1 1 Input sub5-TP1 B-TP1 0 0 1 1 Input sub6-TP1 B-TP1 0 0 1 1 Input sub1-TP2 A-TP2 -1 0 0 0 Input sub2-TP2 A-TP2 -1 0 0 0 Input sub3-TP2 A-TP2 -1 0 0 0 Input sub4-TP2 B-TP2 0 0 -1 0 Input sub5-TP2 B-TP2 0 0 -1 0 Input sub6-TP2 B-TP2 0 0 -1 0 Input sub1-TP3 A-TP3 0 -1 0 0 Input sub2-TP3 A-TP3 0 -1 0 0 Input sub3-TP3 A-TP3 0 -1 0 0 Input sub4-TP3 B-TP3 0 0 0 -1 Input sub5-TP3 B-TP3 0 0 0 -1 Input sub6-TP3 B-TP3 0 0 0 -1 Question 1 - My question is how do I setup the contrasts for the different treatment arms - A-TP1-vs-B-TP1 A-TP2-vs-B-TP2 A-TP3-vs-B-TP3 Question 2 - Also I have age and cognitive scores for each timepoint. How do I add those to the contrast file ? Thank you for the help, Regards Rito On Mon, Jul 12, 2021 at 10:51 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Yes, it will work on both. If you use a table, then pass the table with > --table tablefile instead of --y > > On 7/12/2021 7:54 AM, Ritobrato Datta wrote: > > External Email - Use Caution > Good morning, > > Thanks Doug for the answers. Quick naive question. The analyses I want to > perform are on volumetric data parcellated using aseg and not surface data. > > Does mri_glmfit work with the output of the asegstats2table or on > voxelwise FA maps ? > > Many thanks > > Rito > > On Fri, Jul 9, 2021 at 4:04 PM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> >> >> On 7/9/2021 11:44 AM, Ritobrato Datta wrote: >> >> External Email - Use Caution >> >> Hi All, >> >> >> I have the following data – >> >> >> >> I have 205 subjects - each subject was imaged at 3 timepoints (baseline, >> followup 1 and followup 2) >> >> The 205 subjects are split in two treatment arms with 100 subjects in the >> first one and 105 subjects in the second one. >> >> >> >> For each timepoint, I have created FA maps in their native diffusion >> space. >> >> I have also extracted the mean FA maps for 187 ROIs using mri_segstats. >> >> For each timepoint, I have saved the results as a matrix (FA in 187 ROIs >> x 205 subjects) in a text file. >> >> So I have three files for the three timepoints. >> >> >> >> I have the age and cognitive score for each subject at each timepoint. >> And their gender. >> >> >> >> I want to answer the following questions – >> >> >> >> 1. Do the baseline FA correlate with the corresponding cognitive >> score at baseline ? >> >> This is a straight forward group analysis, so see *MailScanner has >> detected a possible fraud attempt from "secure-web.cisco.com" claiming to >> be* >> https://secure-web.cisco.com/1ZfuNLBplQ19J4Wa1OXL7_1Y-rjJvSIXBqjTAW29FzcfeaaeqYgi0u6AZHG4kchpYX7m8HUM6XmVdqjHa9z5fjgkoVWMMujW9D0JREjDnlQXxdpqo51YEvJar6CDUr32K2gt-FeJmb_hFjHreiACK0avb3oaIThmHLWgKEItcFeL_JI90lJdajfYMYESVaKlImLIEy6Mg1sn9-7c-BtkvhVRfKkdcL-VgQwsf9j_1VJzHr1Ii-tzV7Y5kxYlKl2PVJsQFWGHJoS2wb7RJSh0ChA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples >> <https://secure-web.cisco.com/1kTEkM43RMM06eViww_c18Pc-0P94xql3L2qK8iLarzzC3y3ZVsJIyVlzwF_FfFDswP_67I4PBLfYANWVTXuX-4X-dgKz6-k68o_AL_cvOJiFFFtpwIkd_pFO6m_tuaJtslVIIdmaO4umpQP9t8aMp-MPFEXKVDhKSsBgBNLINu7lLfDwLYKxiP2ZBbWcSlnNZ_KCTA3HDdKNI3PG_H6HTqTiwoC5vQjUicP6uxqYdn-HGl01ZnCt5V89LbOE3usywXIQtA_sZ4MgIcXGQDbj2g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples> >> (maybe >> the Two Groups (1 Factor, Two Levels), One Covariate >> <https://secure-web.cisco.com/1Rg-kxMT-3fQYeRaisunO8_YESB0oLHn151lBD4p9GXp_k96wsb_0fS3wm9AsXst9uQO9dbqRePqf6ijMZUnk_-eFE6HtBGPMjtgURPbRAk_5EC3Q0F3VX-mhUssaYthkDfBZtL6yv0bGjJhKRQulYDXsfvmbpUWl4VH11l7cdQD2p1m_QzCr5liecQPY6UPX6OiGxGITQdALxOE9JdoIyXv0aJ_ozwU_Lw9H2pA2lcXdQEb4RTfOartXbc2P58SNR1mmH4DIzvfp7MxOG1oqRA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdf2G1V>) >> >> >> >> 1. I am interested in testing whether the FA changed significantly >> across the different timepoints and does that relate to the change in the >> cognitive score >> >> See *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1e-onyc_rYKGqWksTToqKP4uqWespCReuPBJOrGcNOZRRibbQSE-yW4NeksFQgQhhkqsb_hk1A_HC0BoxjePQa6hZyg_ZEjAvfREbvB9zqBJwzLSDP9mp0FRHMvH-eHcu3fvzLT3QbULVJgexy0fUD-CNkHWJev5lPNkDEy6Sl-czpF7ITgXHN-i2Fx-P6NdDG2gcQuHLdsQxpFb111wWY4aBe1aW9GlBoLq7cfeQtVV036aRa02ZfqgSNdw07yC3lva5uE-QLm7Y6KJ42kgBIQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova >> <https://secure-web.cisco.com/1l3pHvz1wZceoR8e52Wja_MsMNej9vi7VZZmS8c-z4MS9JGbI3TYJJMikCYf0s7kjh03rhGqRoz4Nqw5FjnWspM8jPaxx5vhTf6cgH1nVEw8kZAyGg-kIVm5tQNWqRiQ-S-cYslSRjWA5zKzXqqcgwKeSWShLW2aw-XRuSrV9IBOmdGQq2pERdmOAqXTVIKchIwtjPqefKoRqoYe4OZ6h_wlLLnBEFs_BJGv4A9Eabyq07igMiO8NeE8VYMkEhQFl0KlX_VyWmlAm-N28VS8hcg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova> >> >> >> 1. Is there an effect of treatment on this change in FA across time ? >> >> Also see *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1e-onyc_rYKGqWksTToqKP4uqWespCReuPBJOrGcNOZRRibbQSE-yW4NeksFQgQhhkqsb_hk1A_HC0BoxjePQa6hZyg_ZEjAvfREbvB9zqBJwzLSDP9mp0FRHMvH-eHcu3fvzLT3QbULVJgexy0fUD-CNkHWJev5lPNkDEy6Sl-czpF7ITgXHN-i2Fx-P6NdDG2gcQuHLdsQxpFb111wWY4aBe1aW9GlBoLq7cfeQtVV036aRa02ZfqgSNdw07yC3lva5uE-QLm7Y6KJ42kgBIQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova >> <https://secure-web.cisco.com/1l3pHvz1wZceoR8e52Wja_MsMNej9vi7VZZmS8c-z4MS9JGbI3TYJJMikCYf0s7kjh03rhGqRoz4Nqw5FjnWspM8jPaxx5vhTf6cgH1nVEw8kZAyGg-kIVm5tQNWqRiQ-S-cYslSRjWA5zKzXqqcgwKeSWShLW2aw-XRuSrV9IBOmdGQq2pERdmOAqXTVIKchIwtjPqefKoRqoYe4OZ6h_wlLLnBEFs_BJGv4A9Eabyq07igMiO8NeE8VYMkEhQFl0KlX_VyWmlAm-N28VS8hcg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FRepeatedMeasuresAnova> >> >> >> >> Can you please suggest what programs in freesurfer will allow me to test >> these questions on both voxelwise and ROI wise ? >> >> >> Many thanks for your help and guidance, >> >> >> Regards >> >> >> Rito >> >>
GroupDescriptorFile 1 Title A-Vs-B-Long Class A-TP1 Class B-TP1 Class A-TP2 Class B-TP2 Class A-TP3 Class B-TP3 Variables A-TP1-vs-A-TP2 A-TP1-vs-A-TP3 B-TP1-vs-B-TP2 B-TP1-vs-B-TP3 A-TP1-vs-B-TP1 A-TP2-vs-B-TP2 A-TP3-vs-B-TP3 Input sub1-TP1 A-TP1 1 1 0 0 Input sub2-TP1 A-TP1 1 1 0 0 Input sub3-TP1 A-TP1 1 1 0 0 Input sub4-TP1 B-TP1 0 0 1 1 Input sub5-TP1 B-TP1 0 0 1 1 Input sub6-TP1 B-TP1 0 0 1 1 Input sub1-TP2 A-TP2 -1 0 0 0 Input sub2-TP2 A-TP2 -1 0 0 0 Input sub3-TP2 A-TP2 -1 0 0 0 Input sub4-TP2 B-TP2 0 0 -1 0 Input sub5-TP2 B-TP2 0 0 -1 0 Input sub6-TP2 B-TP2 0 0 -1 0 Input sub1-TP3 A-TP3 0 -1 0 0 Input sub2-TP3 A-TP3 0 -1 0 0 Input sub3-TP3 A-TP3 0 -1 0 0 Input sub4-TP3 B-TP3 0 0 0 -1 Input sub5-TP3 B-TP3 0 0 0 -1 Input sub6-TP3 B-TP3 0 0 0 -1
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