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Ritobrato Datta

9 Jul 2021 9 Jul '21

11:44 a.m.

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 ? 2. 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 3. Is there an effect of treatment on this change in FA across time ?

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

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Douglas N. Greve

9 Jul 9 Jul

4:04 p.m.

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 –

Do the baseline FA correlate with the corresponding cognitive score at baseline ?

This is a straight forward group analysis, so see https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples (maybe the Two Groups (1 Factor, Two Levels), One Covariate https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V)

...

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 https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova

...

Is there an effect of treatment on this change in FA across time ?

Also see https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova

...

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Ritobrato Datta

12 Jul 12 Jul

7:54 a.m.

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 dgreve@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 –

Do the baseline FA correlate with the corresponding cognitive score

at baseline ?

This is a straight forward group analysis, so see https://secure-web.cisco.com/1kTEkM43RMM06eViww_c18Pc-0P94xql3L2qK8iLarzzC3y... (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)

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 https://secure-web.cisco.com/1l3pHvz1wZceoR8e52Wja_MsMNej9vi7VZZmS8c-z4MS9JG...

Is there an effect of treatment on this change in FA across time ?

Also see https://secure-web.cisco.com/1l3pHvz1wZceoR8e52Wja_MsMNej9vi7VZZmS8c-z4MS9JG...

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

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/1moeXAgkPssPWfOwvT-j_41VwfQen83rc1O8vdXW0CCxxP-... 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 http://secure-web.cisco.com/1L9OTZlPXKPYyCo8cU1NWwXNesxVrClv63JnJA6LTTk5uvsp... . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

On Fri, Jul 9, 2021 at 11:44 AM Ritobrato Datta ribrainsurf@gmail.com wrote:

...

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 –

Do the baseline FA correlate with the corresponding cognitive score

at baseline ? 2. 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 3. Is there an effect of treatment on this change in FA across time ?

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

Douglas N. Greve

10:50 a.m.

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 <dgreve@mgh.harvard.edu mailto:dgreve@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://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
<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://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
<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://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
<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


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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Please note that this e-mail is not secure (encrypted).  If you do
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On Fri, Jul 9, 2021 at 11:44 AM Ritobrato Datta <ribrainsurf@gmail.com mailto:ribrainsurf@gmail.com> wrote:

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 ?
 2. 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
 3. Is there an effect of treatment on this change in FA across time ?

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Ritobrato Datta

13 Jul 13 Jul

11:07 a.m.

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 dgreve@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 dgreve@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 –

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-rjJvSIXBqjTAW29Fzcfeaa... 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)

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_rYKGqWksTToqKP4uqWespCReuPBJOrGcNOZRRib... 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

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_rYKGqWksTToqKP4uqWespCReuPBJOrGcNOZRRib... 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

Douglas N. Greve

15 Jul 15 Jul

11:57 a.m.

For A-TP1-vs-B-TP1, you just create a contrast (not a variable in the FSGD). The design matrix from your FSGD will have 6+4=10 regressors. The contrast for A-TP1-vs-B-TP1 would then be 1 -1 0 0 0 0 0 0 0 0 This computes the difference between Class A-TP1 and B-TP1

On 7/13/2021 11:07 AM, Ritobrato Datta wrote:

...

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 <dgreve@mgh.harvard.edu mailto:dgreve@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
<dgreve@mgh.harvard.edu <mailto:dgreve@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://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
    <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://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
    <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://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
    <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

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Douglas N. Greve
Ritobrato Datta
Ritobrato Datta