[Freesurfer] Paired Analysis Questions

2019-04-08 Thread brain health 
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Dear Dr. Greve:

Thank you so much for your time and help. I am working on the Paired
Analysis that you suggested. Very appreciated!

I am interested if there are different within-group changes in brain
structure for an Intervention (PA) and Control (C) group.

Does the paired-diff.fsgd file (peek below) look correct?
PAC Groups
Class Main
Variables Group
Input sub107 Main PA
Input sub112 Main PA
Input sub113 Main C
Input sub118 Main PA
Input sub131 Main C
Input sub132 Main C
Input sub136 Main C


What would be the contrast of interest to include for my question?

Just want to make sure I am running the correct model.

I am also reading the guide about how to interpret the results of the
mri_glmfit commands (e.g.,
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit). Is there another
guide to follow regarding the output of the Paired Analysis?

I appreciate your guidance!
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[Freesurfer] Paired Analysis Questions

2019-07-13 Thread FAST Study 
External Email - Use Caution

Dear Dr. Greve: Hooray! All has run successfully for the Paired Analysis (
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis).
I used the [1 0] contrast to examine whether there are different
within-group changes in brain structure for an Intervention (PA) and
Control (C) group..
After running —

*mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh
--fsgd paired-diff.fsgd --C mean.mtx --surface fsaverage lh*
(Full terminal output below)

*Will you help me read the output of mri_glmfit?* I am not sure what to
check for results. Are the results corrected for multiple comparisons?
THANKS.

*mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh
--fsgd paired-diff.fsgd --C mean.mtx --surface fsaverage lh*
gdfRead(): reading paired-diff.fsgd
INFO: ignoring tag subs
INFO: gd2mtx_method is dods
Reading source surface
/Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.984375
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt
cmdline mri_glmfit.bin --glmdir lh.paired-diff --y
lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx
--surface fsaverage lh
sysname  Darwin
hostname laurachaddock.vp.illinois.edu
machine  x86_64
user laurachaddock
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
   
/Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/lh.paired-diff.thickness.sm05.mgh
logyflag 0
usedti  0
FSGD paired-diff.fsgd
labelmask
 
/Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.paired-diff
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.paired-diff
Loading y from
/Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/lh.paired-diff.thickness.sm05.mgh
  ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to lh.paired-diff/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1.29787
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149946 voxels in mask
Saving mask to lh.paired-diff/mask.mgh
Reshaping mriglm->mask...
search space = 74607.309418
DOF = 106
Starting fit and test
Fit completed in 0.0936 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.984663, ar1std=0.005741, gstd=3.255205, fwhm=7.665423
Writing results
 mean
   maxvox sig=3.95093  F=16.1054  at  index 115412 0 0seed=1563757270
mri_glmfit done
bash-3.2$
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Re: [Freesurfer] Paired Analysis Questions

2019-04-09 Thread Greve, Douglas N.,Ph.D. 

Do you have two groups? If so, then specify
Class PA
Class C
Instead of Class Main.
Then in the input lines use, eg,
Inputsub118PA
Inputsub131C



On 4/8/2019 9:35 PM, brain health wrote:

External Email - Use Caution

Dear Dr. Greve:

Thank you so much for your time and help. I am working on the Paired Analysis 
that you suggested. Very appreciated!

I am interested if there are different within-group changes in brain structure 
for an Intervention (PA) and Control (C) group.

Does the paired-diff.fsgd file (peek below) look 
correct?
PAC Groups
Class Main
Variables Group
Input sub107 Main PA
Input sub112 Main PA
Input sub113 Main C
Input sub118 Main PA
Input sub131 Main C
Input sub132 Main C
Input sub136 Main C


What would be the contrast of interest to include for my question?

Just want to make sure I am running the correct model.

I am also reading the guide about how to interpret the results of the 
mri_glmfit commands (e.g., 
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit). Is there another guide 
to follow regarding the output of the Paired Analysis?

I appreciate your guidance!




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Re: [Freesurfer] Paired Analysis Questions

2019-07-13 Thread Greve, Douglas N.,Ph.D. 


On 7/13/2019 11:47 AM, FAST Study wrote:

External Email - Use Caution

Dear Dr. Greve: Hooray! All has run successfully for the Paired Analysis 
(https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis).
I used the [1 0] contrast to examine whether there are different within-group 
changes in brain structure for an Intervention (PA) and Control (C) group..
After running —
mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd 
paired-diff.fsgd --C mean.mtx --surface fsaverage lh
(Full terminal output below)
Will you help me read the output of mri_glmfit? I am not sure what to check for 
results. Are the results corrected for multiple comparisons? THANKS.
It is not corrected for multiple comparisons. Use mri_glmfit-sim (there is a 
tutorial for this). At this point, you can either do multiple comp corrections 
or visualize the uncorrected maps. There is not a lot to talk about in the 
terminal output.

mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd 
paired-diff.fsgd --C mean.mtx --surface fsaverage lh
gdfRead(): reading paired-diff.fsgd
INFO: ignoring tag subs
INFO: gd2mtx_method is dods
Reading source surface 
/Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.984375
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt
cmdline mri_glmfit.bin --glmdir lh.paired-diff --y 
lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx 
--surface fsaverage lh
sysname  Darwin
hostname laurachaddock.vp.illinois.edu
machine  x86_64
user laurachaddock
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/lh.paired-diff.thickness.sm05.mgh
logyflag 0
usedti  0
FSGD paired-diff.fsgd
labelmask  
/Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.paired-diff
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.paired-diff
Loading y from 
/Volumes/HealthDevelopment/FITKIDS2/FREESURFER/Pairedt/lh.paired-diff.thickness.sm05.mgh
  ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to lh.paired-diff/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1
Matrix condition is 1.29787
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149946 voxels in mask
Saving mask to lh.paired-diff/mask.mgh
Reshaping mriglm->mask...
search space = 74607.309418
DOF = 106
Starting fit and test
Fit completed in 0.0936 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.984663, ar1std=0.005741, gstd=3.255205, fwhm=7.665423
Writing results
 mean
   maxvox sig=3.95093  F=16.1054  at  index 115412 0 0seed=1563757270
mri_glmfit done
bash-3.2$



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