Re: [Freesurfer] Group Analysis - 4 groups 3 covariates

[Douglas N. Greve]

On 11/29/2023 2:16 PM, Tejaswi D. Sudhakar wrote:


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Hi,

I would like to run a group analysis on 4 groups (patientM, patientF, 
controlM, controlF) with 3 covariates (age, cogscore1, cogscore2).


I am running with dods - so I would have 16 total regressors. How 
would I create contrast matrices for this?


I have this so far:

0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0

0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0

0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5

Yes, that will test for a difference between patients and controls for 
offset, cogscore1, and cogscore2


Secondly, I created lh.train.thickness.10B.mgh since the initial run 
was not qcached. How can I check if there is an error with this file?


There is not really a procedure for this. I guess you could look at the 
rstd.mgh map in the output mri_glmfit. The rstd is the std dev of the 
residual error. If there are some regions that are much higher than 
others it could represent a problem, but I don't have much more guidance 
than that. You can also look at the mask.mgh for any areas that are 0 
that should not (eg, the medial wall will be 0, but that should be the case)


Thanks in advance.


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[Freesurfer] Group Analysis - 4 groups 3 covariates

[Tejaswi D. Sudhakar]

External Email - Use Caution

Hi,

I would like to run a group analysis on 4 groups (patientM, patientF, controlM, 
controlF) with 3 covariates (age, cogscore1, cogscore2).

I am running with dods - so I would have 16 total regressors. How would I 
create contrast matrices for this?

I have this so far:
0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0

0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 0 0

0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5

Secondly, I created lh.train.thickness.10B.mgh since the initial run was not 
qcached. How can I check if there is an error with this file?

Thanks in advance.


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Re: [Freesurfer] Group analysis question

[Douglas N. Greve]

So you are trying to predict the neuropsych battery from brain 
measurement? This is not how mri_glmfit is usually used, but it is just 
a GLM so it is possible. You'd have to set up a table for the --table 
input. You can try running asegstats2table to get an example table, then 
you'd just set up your FSGD with the brain measurements and other 
covariates as variables. Traditionally, someone trying to do this would 
use R or SPSS.


On 10/31/2023 5:18 PM, Nicolette Barber wrote:


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Hello,

I am working on a project using FreeSurfer, and I am trying to set up 
a whole brain group analysis. However, I am not sure how to set up the 
FSDG files, etc., as my dependent variable is not a cortical 
measurement. My dependent variable is a neuropsychological battery, 
culture, and brain measurement are my independent, and my covariate is 
ICV.


I have been trying to figure this out for a while now. Is there a way 
to change the dependent variable for mriglm_fit? And if so, how would 
I set this up? I am using version 6.


Thank you,
Nicolette


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[Freesurfer] Group analysis question

[Nicolette Barber]

External Email - Use Caution

Hello,

I am working on a project using FreeSurfer, and I am trying to set up a
whole brain group analysis. However, I am not sure how to set up the FSDG
files, etc., as my dependent variable is not a cortical measurement. My
dependent variable is a neuropsychological battery, culture, and brain
measurement are my independent, and my covariate is ICV.

I have been trying to figure this out for a while now. Is there a way to
change the dependent variable for mriglm_fit? And if so, how would I set
this up? I am using version 6.

Thank you,
Nicolette
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Re: [Freesurfer] Group Analysis - glmfit results

[Douglas N. Greve]

Assuming that your input is timepoint2-timepoint1, your contrast will 
realize C = (INT2-INT1)-(CON2-CON1) as a final value.


On 9/6/2022 12:42 AM, rstei...@student.ubc.ca wrote:


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Thank you for getting back to me. You are correct in your in that the 
contrast is C = (INT2-INT1)-(CON2-CON1). The measure of interest is SPC.


For the complete test we are trying to determine between group 
differences in cortical thickness, adjusting for covariates (age, sex, 
and  MoCA). I was hoping to visualize this differencegraphically using 
the cache.th13.abs.y.ocn.dat file output.


This is our FSGD:

GroupDescriptorFile 1
Title Between-group
Class int_male
Class int_female
Class con_male
Class con_female
Variables age moca
Input 001.MR int_male  30     25
Input 002.MR int_female    40     22
Input 003.MR con_male  60     29
Input 004.MR con_female    60     21
    …
And this is the contrast matrix
+0.5 +0.5 -0.5 -0.5 +0 +0 +0 +0 +0 +0 +0 +0

Thank you,


Ryan G. Stein

MSc Student, Rehabilitation Sciences

Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia | Vancouver Campus 
| Musqueam Traditional Territory



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* August 28, 2022 12:45:22 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Group Analysis - glmfit results
[*CAUTION:* Non-UBC Email]

Since this is longitudinal, I'm assuming that your contrast is 
actually something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 
and 2 the the time points. As you suggest, both (INT2-INT1) and 
(CON2-CON1) might both be less than 0, but if INT is less negative 
than CON, then C will be positive and everything is working as it 
should (ie, there is not a problem or discrepancy here). What is the 
(complete) test that you are trying to accomplish?




On 8/23/2022 3:10 PM, rstei...@student.ubc.ca wrote:


External Email - Use Caution

Hello Freesurfer Team,

I recently ran analysis to compare change in cortical thickness 
between an Intervention and Control group longitudinally. The 
contrast is set up as INT-CON, and therefore I would interpret a 
positive change as the intervention having a greater increase in 
cortical thickness or less atrophy than the control group.


The cluster that survived the Monte-Carlo simulation showed a 
positive difference in the LH superior parietal region when running 
both an ‘abs’ and ‘pos’ simulation (these showed the same 
cluster.summary outputs). There was not a significant cluster when 
running the ‘neg’ simulation. When I compared the mean change in 
thickness between groups (cache.th13.abs.y.ocn.dat file), it showed 
that the control group experienced less atrophy than the intervention 
despite having a positive cluster output.


One possible solution I considered is accounting for baseline 
differences between groups when looking at mean change. Does glmfit 
control for baseline cortical thickness in the cluster analysis that 
is not accounted for in the mean change values from the 
cache.th13.abs.y.ocn.dat file? Is there another possible explanation 
for this discrepancy?


Thank you in advance,

Ryan S


Ryan G. Stein

MSc Student, Rehabilitation Sciences

Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia | Vancouver Campus 
| Musqueam Traditional Territory



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Re: [Freesurfer] Group Analysis - glmfit results

[rstei...@student.ubc.ca]

External Email - Use Caution

Thank you for getting back to me. You are correct in your in that the contrast 
is C = (INT2-INT1)-(CON2-CON1). The measure of interest is SPC.

For the complete test we are trying to determine between group differences in 
cortical thickness, adjusting for covariates (age, sex, and  MoCA). I was 
hoping to visualize this difference graphically using the 
cache.th13.abs.y.ocn.dat file output.

This is our FSGD:

GroupDescriptorFile 1
Title Between-group
Class int_male
Class int_female
Class con_male
Class con_female
Variables age moca
Input 001.MR int_male  30 25
Input 002.MR int_female40 22
Input 003.MR con_male  60 29
Input 004.MR con_female60 21
…

And this is the contrast matrix
+0.5 +0.5 -0.5 -0.5 +0 +0 +0 +0 +0 +0 +0 +0

Thank you,


Ryan G. Stein

MSc Student, Rehabilitation Sciences

Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia | Vancouver Campus | Musqueam Traditional 
Territory



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: August 28, 2022 12:45:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Group Analysis - glmfit results

[CAUTION: Non-UBC Email]
Since this is longitudinal, I'm assuming that your contrast is actually 
something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the the time 
points. As you suggest, both (INT2-INT1) and (CON2-CON1) might both be less 
than 0, but if INT is less negative than CON, then C will be positive and 
everything is working as it should (ie, there is not a problem or discrepancy 
here). What is the (complete) test that you are trying to accomplish?



On 8/23/2022 3:10 PM, rstei...@student.ubc.ca<mailto:rstei...@student.ubc.ca> 
wrote:

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Hello Freesurfer Team,

I recently ran analysis to compare change in cortical thickness between an 
Intervention and Control group longitudinally. The contrast is set up as 
INT-CON, and therefore I would interpret a positive change as the intervention 
having a greater increase in cortical thickness or less atrophy than the 
control group.

The cluster that survived the Monte-Carlo simulation showed a positive 
difference in the LH superior parietal region when running both an ‘abs’ and 
‘pos’ simulation (these showed the same cluster.summary outputs). There was not 
a significant cluster when running the ‘neg’ simulation. When I compared the 
mean change in thickness between groups (cache.th13.abs.y.ocn.dat file), it 
showed that the control group experienced less atrophy than the intervention 
despite having a positive cluster output.

One possible solution I considered is accounting for baseline differences 
between groups when looking at mean change. Does glmfit control for baseline 
cortical thickness in the cluster analysis that is not accounted for in the 
mean change values from the cache.th13.abs.y.ocn.dat file? Is there another 
possible explanation for this discrepancy?

Thank you in advance,

Ryan S


Ryan G. Stein

MSc Student, Rehabilitation Sciences

Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia | Vancouver Campus | Musqueam Traditional 
Territory




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Re: [Freesurfer] Group Analysis - glmfit results

[Douglas N. Greve]

Since this is longitudinal, I'm assuming that your contrast is actually 
something like contrast C = (INT2-INT1)-(CON2-CON1) where 1 and 2 the 
the time points. As you suggest, both (INT2-INT1) and (CON2-CON1) might 
both be less than 0, but if INT is less negative than CON, then C will 
be positive and everything is working as it should (ie, there is not a 
problem or discrepancy here). What is the (complete) test that you are 
trying to accomplish?




On 8/23/2022 3:10 PM, rstei...@student.ubc.ca wrote:


External Email - Use Caution

Hello Freesurfer Team,

I recently ran analysis to compare change in cortical thickness 
between an Intervention and Control group longitudinally. The contrast 
is set up as INT-CON, and therefore I would interpret a positive 
change as the intervention having a greater increase in cortical 
thickness or less atrophy than the control group.


The cluster that survived the Monte-Carlo simulation showed a positive 
difference in the LH superior parietal region when running both an 
‘abs’ and ‘pos’ simulation (these showed the same cluster.summary 
outputs). There was not a significant cluster when running the ‘neg’ 
simulation. When I compared the mean change in thickness between 
groups (cache.th13.abs.y.ocn.dat file), it showed that the control 
group experienced less atrophy than the intervention despite having a 
positive cluster output.


One possible solution I considered is accounting for baseline 
differences between groups when looking at mean change. Does glmfit 
control for baseline cortical thickness in the cluster analysis that 
is not accounted for in the mean change values from the 
cache.th13.abs.y.ocn.dat file? Is there another possible explanation 
for this discrepancy?


Thank you in advance,

Ryan S


Ryan G. Stein

MSc Student, Rehabilitation Sciences

Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia | Vancouver Campus 
| Musqueam Traditional Territory



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[Freesurfer] Group Analysis - glmfit results

[rstei...@student.ubc.ca]

External Email - Use Caution

Hello Freesurfer Team,

I recently ran analysis to compare change in cortical thickness between an 
Intervention and Control group longitudinally. The contrast is set up as 
INT-CON, and therefore I would interpret a positive change as the intervention 
having a greater increase in cortical thickness or less atrophy than the 
control group.

The cluster that survived the Monte-Carlo simulation showed a positive 
difference in the LH superior parietal region when running both an ‘abs’ and 
‘pos’ simulation (these showed the same cluster.summary outputs). There was not 
a significant cluster when running the ‘neg’ simulation. When I compared the 
mean change in thickness between groups (cache.th13.abs.y.ocn.dat file), it 
showed that the control group experienced less atrophy than the intervention 
despite having a positive cluster output.

One possible solution I considered is accounting for baseline differences 
between groups when looking at mean change. Does glmfit control for baseline 
cortical thickness in the cluster analysis that is not accounted for in the 
mean change values from the cache.th13.abs.y.ocn.dat file? Is there another 
possible explanation for this discrepancy?

Thank you in advance,

Ryan S


Ryan G. Stein

MSc Student, Rehabilitation Sciences

Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
University of British Columbia | Vancouver Campus | Musqueam Traditional 
Territory

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Re: [Freesurfer] Group Analysis - FSGD and Contrast

[Douglas N. Greve]

yes, that is the correct interpretation

On 7/16/2022 1:00 PM, Boa Sorte Silva, Narlon wrote:


External Email - Use Caution

Dear experts,

I am conducting a group analysis and wanted to confirm that the set up 
below accurately addresses our research question. Thanks for your 
help, much appreciated!


Background:

  * We have two groups (intervention vs control) and two timepoints
(pre vs post)
  * Our data have already been processed and stacked with
*long_mris_slopes* where pc1 is the measure of interest (post - pre).
  * Our covariates are sex (male vs female), age, and MMSE scores.
  * Thus, our model has 4 groups (2 factors/2 levels):
  o int_male
  o int_female
  o con_male
  o con_female
  * We’re using *DODS*
  * We’re running the analysis with *mri_glmfit* in the Longitudinal
Two Stage Model

As such, we want test whether there are greater changes in the 
intervention group vs control group in the pc1 measure, adjusting for 
the influence of sex, age, and MMSE.


This is our FSGD:

GroupDescriptorFile 1

Title Between-group

Class int_male

Class int_female

Class con_male

Class con_female

Variables age mmse

Input 001.MR int_male  30     25

Input 002.MR int_female    40     22

Input 003.MR con_male  60     29

Input 004.MR con_female    60     21

    …

And this is the contrast matrix

+0.5 +0.5 -0.5 -0.5 +0 +0 +0 +0 +0 +0 +0 +0

With the above contrast matrix, our interpretation would be:

  * Intervention > control = positive result
  * Intervention < control = negative result

Is this the correct set up and interpretation?

Thanks for taking the time,

Best regards,

Nárlon Cássio

*Nárlon Cássio Boa Sorte Silva* PhD (He, Him, His)

CIHR and MSHR BC/PARF Postdoctoral Research Fellow

Aging, Mobility, and Cognitive Health Lab

Djavad Mowafaghian Centre for Brain Health

Department of Physical Therapy, Faculty of Medicine

University of British Columbia

Vancouver, Canada

Twitter: @BoaNarlon


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Re: [Freesurfer] Group Analysis - FSGD and Contrast

[Boa Sorte Silva, Narlon]

External Email - Use Caution

Hi there,
Just following up on this

Thanks,
Nárlon Cássio

Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSHR BC/PARF Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon

On Jul 16, 2022, at 10:00 AM, Boa Sorte Silva, Narlon 
mailto:narlon.si...@ubc.ca>> wrote:

[CAUTION: Non-UBC Email]

External Email - Use Caution

Dear experts,

I am conducting a group analysis and wanted to confirm that the set up below 
accurately addresses our research question. Thanks for your help, much 
appreciated!

Background:

  *   We have two groups (intervention vs control) and two timepoints (pre vs 
post)
  *   Our data have already been processed and stacked with long_mris_slopes 
where pc1 is the measure of interest (post - pre).
  *   Our covariates are sex (male vs female), age, and MMSE scores.
  *   Thus, our model has 4 groups (2 factors/2 levels):
 *   int_male
 *   int_female
 *   con_male
 *   con_female
  *   We’re using DODS
  *   We’re running the analysis with mri_glmfit in the Longitudinal Two Stage 
Model

As such, we want test whether there are greater changes in the intervention 
group vs control group in the pc1 measure, adjusting for the influence of sex, 
age, and MMSE.

This is our FSGD:
GroupDescriptorFile 1
Title Between-group
Class int_male
Class int_female
Class con_male
Class con_female
Variables age mmse
Input 001.MR int_male  30 25
Input 002.MR int_female40 22
Input 003.MR con_male  60 29
Input 004.MR con_female60 21
…

And this is the contrast matrix
+0.5 +0.5 -0.5 -0.5 +0 +0 +0 +0 +0 +0 +0 +0

With the above contrast matrix, our interpretation would be:

  *   Intervention > control = positive result
  *   Intervention < control = negative result

Is this the correct set up and interpretation?

Thanks for taking the time,
Best regards,
Nárlon Cássio

Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSHR BC/PARF Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon[X]
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[Freesurfer] Group Analysis - FSGD and Contrast

[Boa Sorte Silva, Narlon]

External Email - Use Caution

Dear experts,

I am conducting a group analysis and wanted to confirm that the set up below 
accurately addresses our research question. Thanks for your help, much 
appreciated!

Background:

  *   We have two groups (intervention vs control) and two timepoints (pre vs 
post)
  *   Our data have already been processed and stacked with long_mris_slopes 
where pc1 is the measure of interest (post - pre).
  *   Our covariates are sex (male vs female), age, and MMSE scores.
  *   Thus, our model has 4 groups (2 factors/2 levels):
 *   int_male
 *   int_female
 *   con_male
 *   con_female
  *   We’re using DODS
  *   We’re running the analysis with mri_glmfit in the Longitudinal Two Stage 
Model

As such, we want test whether there are greater changes in the intervention 
group vs control group in the pc1 measure, adjusting for the influence of sex, 
age, and MMSE.

This is our FSGD:
GroupDescriptorFile 1
Title Between-group
Class int_male
Class int_female
Class con_male
Class con_female
Variables age mmse
Input 001.MR int_male  30 25
Input 002.MR int_female40 22
Input 003.MR con_male  60 29
Input 004.MR con_female60 21
…

And this is the contrast matrix
+0.5 +0.5 -0.5 -0.5 +0 +0 +0 +0 +0 +0 +0 +0

With the above contrast matrix, our interpretation would be:

  *   Intervention > control = positive result
  *   Intervention < control = negative result

Is this the correct set up and interpretation?

Thanks for taking the time,
Best regards,
Nárlon Cássio

Nárlon Cássio Boa Sorte Silva PhD (He, Him, His)
CIHR and MSHR BC/PARF Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon[X]
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Re: [Freesurfer] Group Analysis

[Douglas N. Greve]

Can you send the log file for the 2nd mris_preproc command?

On 2/8/2021 4:52 PM, Larissa Bechtle wrote:


External Email - Use Caution

Hi everybody,
I ran the following commands which worked out fine for my Group Analysis.
Just like in the wiki-Tutorial available I focused on the thickness of 
my probands brains at first.


setenv FREESURFER_HOME /Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.csh

setenv SUBJECTS_DIR /Users/Forschung/Desktop/Larissa/Gewalt

recon-all -s ab35 –qcache

mris_preproc --fsgd FSGD.fsgd --cache-in thickness.fwhm10.fsaverage 
--target fsaverage --hemi lh --out lh.gewalt.10.mgh


mri_glmfit --y lh.gewalt.10.mgh --fsgd FSGD.fsgd dods --C 
lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir 
leftuncorrected.glmdir


freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=leftuncorrected.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5-viewport 
3d


Currently I am tryig to run the same Group Analysis but now focusing 
on the volume instead.
Thus I tried to change my commands. I ended up with the same image as 
in my previous Group Analysis (which focused on  hickness instead of 
volume) and I dont really get why.

I would be very grateful for any support.
Best wishes
Larissa

setenv FREESURFER_HOME /Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.csh

setenv SUBJECTS_DIR /Users/Forschung/Desktop/Larissa/Gewalt

mris_preproc --fsgd FSGD.fsgd --cache-in volume.fwhm10.fsaverage 
--target fsaverage --hemi lh --out lh.gewalt_volume.10.mgh


mri_glmfit --y lh.gewalt_volume.10.mgh --fsgd FSGD.fsgd dods --C 
lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir 
lefttuncorrected_volume.glmdir


freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=leftuncorrected_volume.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5-viewport 
3d



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[Freesurfer] Group Analysis

[Larissa Bechtle]

External Email - Use CautionHi everybody,

 

I ran the following commands which worked out fine for my Group Analysis.

Just like in the wiki-Tutorial available I focused on the thickness of my probands brains at first.  

 


setenv FREESURFER_HOME /Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.csh

setenv SUBJECTS_DIR /Users/Forschung/Desktop/Larissa/Gewalt

recon-all -s ab35 –qcache

mris_preproc --fsgd FSGD.fsgd --cache-in thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gewalt.10.mgh

mri_glmfit --y lh.gewalt.10.mgh --fsgd FSGD.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir leftuncorrected.glmdir 

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=leftuncorrected.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5-viewport 3d

 

Currently I am tryig to run the same Group Analysis but now focusing on the volume instead.

Thus I tried to change my commands. I ended up with the same image as in my previous Group Analysis (which focused on  hickness instead of volume) and I dont really get why.

 

I would be very grateful for any support.

 

Best wishes

 

Larissa

 

 


setenv FREESURFER_HOME /Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.csh

setenv SUBJECTS_DIR /Users/Forschung/Desktop/Larissa/Gewalt

mris_preproc --fsgd FSGD.fsgd --cache-in volume.fwhm10.fsaverage --target fsaverage --hemi lh --out lh.gewalt_volume.10.mgh

mri_glmfit --y lh.gewalt_volume.10.mgh --fsgd FSGD.fsgd dods --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lefttuncorrected_volume.glmdir 

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=leftuncorrected_volume.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5-viewport 3d


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Re: [Freesurfer] Group Analysis Question

[Greve, Douglas N.,Ph.D.]

I think that contrast computes Female-Male regressing out Dx and age. If you 
want HC vs MS, then use
-0.5 -0.5 0.5 0.5


On 12/29/2020 4:52 PM, Swanson,Clayton wrote:

External Email - Use Caution

Hi Freesurfer Team,
I am performing an analysis on 23 HC and 26 people with MS and I would like to 
perform the stats appropriately. I would like to control for (or regress out) 
age and sex.  Therefore, I created my FSGD file which has 4 classes (HC_Male, 
HC_Female, MS_Male, MS_Female) with age being the only variable.  My contrast 
for this analysis is: 0.5 -0.5 0.5 -0.5 0 0 0 0. Lastly, I want to run a 
permutation analysis, so I set it up like this:

#!/bin/tcsh
setenv study $argv[1]
foreach meas (thickness volume)
  foreach hemi (lh rh)
foreach smoothness (10)
  foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
mri_glmfit-sim \
  --glmdir {$dir} \
  --perm 1000 1.3 pos \
  --cwp 0.05  \
  --2spaces \
--overwrite
  end
end
  end
end

After running the permutation, my next steps were to view the results in 
Freeview with the command [ freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=perm.th13.pos.sig.cluster.mgh 
] because it’s my understanding that would overlay the cluster-wise corrected 
map and the view I get is an entirely yellow hemisphere. However, there are no 
significant clusters when viewing the perm.th13.pos.sig.cluster.summary, so I 
am a bit confused. Also, when I look at the uncorrected results with the 
sig.mgh file there are a number of spots on the hemisphere.

Does this result mean that there are no cortical thickness differences between 
HC and MS when controlling for Age and Sex?  Or does this result mean something 
different?  What could be the next analysis steps I could perform?

My goals are to assess cortical thickness differences between HC and MS.

Thanks for any help you can provide,

Clayton

Clayton Swanson MS
Graduate Research Assistant & PhD Candidate
Sensorimotor Neuroimaging Laboratory
Colorado State University
Office: (970) 491-6160
clayton.swan...@colostate.edu
(He/Him)




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[Freesurfer] Group Analysis Question

[Swanson,Clayton]

External Email - Use Caution

Hi Freesurfer Team,
I am performing an analysis on 23 HC and 26 people with MS and I would like to 
perform the stats appropriately. I would like to control for (or regress out) 
age and sex.  Therefore, I created my FSGD file which has 4 classes (HC_Male, 
HC_Female, MS_Male, MS_Female) with age being the only variable.  My contrast 
for this analysis is: 0.5 -0.5 0.5 -0.5 0 0 0 0. Lastly, I want to run a 
permutation analysis, so I set it up like this:

#!/bin/tcsh
setenv study $argv[1]
foreach meas (thickness volume)
  foreach hemi (lh rh)
foreach smoothness (10)
  foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
mri_glmfit-sim \
  --glmdir {$dir} \
  --perm 1000 1.3 pos \
  --cwp 0.05  \
  --2spaces \
--overwrite
  end
end
  end
end

After running the permutation, my next steps were to view the results in 
Freeview with the command [ freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=perm.th13.pos.sig.cluster.mgh 
] because it’s my understanding that would overlay the cluster-wise corrected 
map and the view I get is an entirely yellow hemisphere. However, there are no 
significant clusters when viewing the perm.th13.pos.sig.cluster.summary, so I 
am a bit confused. Also, when I look at the uncorrected results with the 
sig.mgh file there are a number of spots on the hemisphere.

Does this result mean that there are no cortical thickness differences between 
HC and MS when controlling for Age and Sex?  Or does this result mean something 
different?  What could be the next analysis steps I could perform?

My goals are to assess cortical thickness differences between HC and MS.

Thanks for any help you can provide,

Clayton

Clayton Swanson MS
Graduate Research Assistant & PhD Candidate
Sensorimotor Neuroimaging Laboratory
Colorado State University
Office: (970) 491-6160
clayton.swan...@colostate.edu
(He/Him)

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Re: [Freesurfer] group analysis

[Greve, Douglas N.,Ph.D.]

For starters, you need to have four classes, HC-Male, HC-Female, CMT-Male, 
CMT-Female and not use gender as a variable. Try that. I would also normalize 
the age and thickness

On 11/24/2020 12:04 PM, Ambulatorio SNA FEDERICO II wrote:

External Email - Use Caution

Dear Freesurfer team,

I'm running a group analysis where I'd like to compare myelination between two 
groups regressing out cortical thickness, age and sex.
My FSGD file is:
GroupDescriptorFile 1
Title Func
Class HC
Class CMT
Variables  Age gender
Input fs_VF HC  46 Female
Input fs_RF HC 24 Female
...

My group.diff.mtx is:
1 -1 0 0 0 0 0

My command line:
 mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd 
age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf 
fsaverage rh --cortex --glmdir 
rh_allbrain_t1t2_group_thickness_age_gender.glmdir

But unfortunately I get this wrong message:
RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd 
age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf 
fsaverage rh --cortex --glmdir 
rh_allbrain_t1t2_group_thickness_age_gender.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.00 (col 5), Max=146.140350 (col 3)
 The scale is much different between columns 5 and 3, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
Column 5,  all values are 0
Column 6,  all values are 0
Columns 5 and 6 are the same


Can you please help me?

Thank you very much
Raf



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Re: [Freesurfer] Group Analysis

[Greve, Douglas N.,Ph.D.]

By "volume" do you mean a surface-based, vertex-wise measure of volume or do 
you mean volume of an ROI?

On 11/19/2020 11:46 AM, Mora, Jocelyn S. wrote:
Hi Sara,

You may want to use asegstats2table. Follow these links to learn more about 
mris_preproc, mri_glmfit, and asegstats2table:

http://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit?highlight=%28asegstats%29

https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table?highlight=%28asegstats%29

Best,
Jocelyn

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Sara Lyn <mailto:saralyn...@gmail.com>
Sent: Wednesday, November 18, 2020 6:37 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Group Analysis


External Email - Use Caution

Hi Freesurfer experts,

I was looking to run the three steps of group analysis-mris preproc, mri 
surf2surf using the measure volume and unsure of how to go about it since the 
wiki page talks about thickness only. I would appreciate any help.

Best,
Sara



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Re: [Freesurfer] Group Analysis

[Greve, Douglas N.,Ph.D.]

Make sure that --meas volume was passed to  mris_preproc was passed (this is 
the usual way you would do this) in which case it makes a jacobian correction. 
The only other thing to do would be to correct for intra-cranial volume. If you 
have 7.X, you can just add --etiv to mris_preproc

On 11/18/2020 6:37 PM, Sara Lyn wrote:

External Email - Use Caution

Hi Freesurfer experts,

I was looking to run the three steps of group analysis-mris preproc, mri 
surf2surf using the measure volume and unsure of how to go about it since the 
wiki page talks about thickness only. I would appreciate any help.

Best,
Sara



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[Freesurfer] group analysis

[Ambulatorio SNA FEDERICO II]

External Email - Use Caution

Dear Freesurfer team,

I'm running a group analysis where I'd like to compare myelination between
two groups regressing out cortical thickness, age and sex.
My FSGD file is:
GroupDescriptorFile 1
Title Func
Class HC
Class CMT
Variables  Age gender
Input fs_VF HC  46 Female
Input fs_RF HC 24 Female
...

My group.diff.mtx is:
1 -1 0 0 0 0 0

My command line:
 mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd
age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf
fsaverage rh --cortex --glmdir
rh_allbrain_t1t2_group_thickness_age_gender.glmdir

*But unfortunately I get this wrong message: *
RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd
age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf
fsaverage rh --cortex --glmdir
rh_allbrain_t1t2_group_thickness_age_gender.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.00 (col 5), Max=146.140350 (col 3)
 The scale is much different between columns 5 and 3, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
Column 5,  all values are 0
Column 6,  all values are 0
Columns 5 and 6 are the same


Can you please help me?

Thank you very much
Raf
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Re: [Freesurfer] Group Analysis {Disarmed}

[Greve, Douglas N.,Ph.D.]

Just use --meas volume instead of --meas area

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Sara Lyn 

Sent: Thursday, November 19, 2020 12:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Group Analysis {Disarmed}


External Email - Use Caution

Hi Jocelyn,

The links talk about measuring thickness and I’m trying to do a volumetric 
Group analysis using Glm.  I was wondering if you could point me towards that.

Sara

On Thursday, November 19, 2020, Mora, Jocelyn S. 
mailto:jsm...@mgh.harvard.edu>> wrote:
Hi Sara,

You may want to use asegstats2table. Follow these links to learn more about 
mris_preproc, mri_glmfit, and asegstats2table:

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Best,
Jocelyn

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Sara Lyn mailto:saralyn...@gmail.com>>
Sent: Wednesday, November 18, 2020 6:37 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Group Analysis


External Email - Use Caution

Hi Freesurfer experts,

I was looking to run the three steps of group analysis-mris preproc, mri 
surf2surf using the measure volume and unsure of how to go about it since the 
wiki page talks about thickness only. I would appreciate any help.

Best,
Sara
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Re: [Freesurfer] Group Analysis {Disarmed}

[Greve, Douglas N.,Ph.D.]

Sorry, meant to say instead of --meas thickness

From: Greve, Douglas N.,Ph.D. 
Sent: Thursday, November 19, 2020 1:01 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Group Analysis {Disarmed}

Just use --meas volume instead of --meas area

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Sara Lyn 

Sent: Thursday, November 19, 2020 12:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Group Analysis {Disarmed}


External Email - Use Caution

Hi Jocelyn,

The links talk about measuring thickness and I’m trying to do a volumetric 
Group analysis using Glm.  I was wondering if you could point me towards that.

Sara

On Thursday, November 19, 2020, Mora, Jocelyn S. 
mailto:jsm...@mgh.harvard.edu>> wrote:
Hi Sara,

You may want to use asegstats2table. Follow these links to learn more about 
mris_preproc, mri_glmfit, and asegstats2table:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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Best,
Jocelyn

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Sara Lyn mailto:saralyn...@gmail.com>>
Sent: Wednesday, November 18, 2020 6:37 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Group Analysis


External Email - Use Caution

Hi Freesurfer experts,

I was looking to run the three steps of group analysis-mris preproc, mri 
surf2surf using the measure volume and unsure of how to go about it since the 
wiki page talks about thickness only. I would appreciate any help.

Best,
Sara
___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Group Analysis {Disarmed}

[Sara Lyn]

External Email - Use Caution

Hi Jocelyn,

The links talk about measuring thickness and I’m trying to do a volumetric
Group analysis using Glm.  I was wondering if you could point me towards
that.

Sara

On Thursday, November 19, 2020, Mora, Jocelyn S. 
wrote:

> Hi Sara,
>
> You may want to use asegstats2table. Follow these links to learn more
> about mris_preproc, mri_glmfit, and asegstats2table:
>
> http://secure-web.cisco.com/1GcyAZ4TLbRGiuwf3mK0o8IKvcNsxwTULArjRsgQ5-qwwWHseO7Av6RqT8xdhHsL8LHTuIoRLCNHWJBGJo8Agt99_QoT95gst9PbZMUpV2KB70uY9UQ9u_d_-hUpKT_FeCzOVvl_lfE4h9bW6yCb5jjb1LQ_MU8B1aU-8LZ-rOZ3Z_UxUqD99IHmZtQtuT3AfjYAQtdNUl3Y-k3Wh8Cxo4TeJbHILfSoBj3GfcLaPCha4Lkm7H-FDht547FiGBuaBs8Z7W9kOgEGho_vHNXh8yQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_preproc
>
> https://secure-web.cisco.com/1OylzWdn9KNXiaXZXnAXy6Y4zKLT3o_SWqfBObqbSeLwwdc8tsdpFt2tbgaY-ZpE74DE_FWqKA1H-7VuWM-jYEKTZp-Ny65io8jvj--7yeL73z9eRk3xlO93UaGBNsja6Sa3X8M_0B6S9ue1xUjhCdq4rEU32tzHnrDZAmbSDQau-qb-nqAw-nWHhqMzuidDzkRMr-r4lJoacIJgr64ig_TueonRzEASSPIyGdi-lTXBy5Jj-XHWqBskYmql34McxnPTEJ_yEr96CR9Gqm2nCHg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_glmfit?
> highlight=%28asegstats%29
>
> https://secure-web.cisco.com/1v3oCpx-Uv895Hjxj-klxnZ5JfvSWRtw-oWz6bxIOFQbCONpO8RheJdg0dRyqYZa4PqaDfJc8acNicFvz5R9bSncZdGGbhCfB6yVa7_6KwYtN9lbb0OupYLTxrLYqiTx2HjlXsbpppU1LruUY4s3JEhSc_hQvATe7qGevs5lDVwCtMTxRVVn2OJXGL3abOdjKN-yG1KE_hL5frEdisidhiiPH9TxCvNFa0TLbAOsM4s7GmxLy5P5fTUvxHL-O9jtRMg3oNmO_qppP5uvufABpjw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fasegstats2table%3Fhighlight%3D%25
> 28asegstats%29
>
> Best,
> Jocelyn
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Sara Lyn <
> saralyn...@gmail.com>
> *Sent:* Wednesday, November 18, 2020 6:37 PM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] Group Analysis
>
>
> External Email - Use Caution
>
> Hi Freesurfer experts,
>
> I was looking to run the three steps of group analysis-mris preproc, mri
> surf2surf using the measure volume and unsure of how to go about it since
> the wiki page talks about thickness only. I would appreciate any help.
>
> Best,
> Sara
>
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Re: [Freesurfer] Group Analysis

[Mora, Jocelyn S.]

Hi Sara,

You may want to use asegstats2table. Follow these links to learn more about 
mris_preproc, mri_glmfit, and asegstats2table:

http://surfer.nmr.mgh.harvard.edu/fswiki/mris_preproc

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit?highlight=%28asegstats%29

https://surfer.nmr.mgh.harvard.edu/fswiki/asegstats2table?highlight=%28asegstats%29

Best,
Jocelyn

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Sara Lyn 

Sent: Wednesday, November 18, 2020 6:37 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Group Analysis


External Email - Use Caution

Hi Freesurfer experts,

I was looking to run the three steps of group analysis-mris preproc, mri 
surf2surf using the measure volume and unsure of how to go about it since the 
wiki page talks about thickness only. I would appreciate any help.

Best,
Sara
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Group Analysis

[Sara Lyn]

External Email - Use Caution

Hi Freesurfer experts,

I was looking to run the three steps of group analysis-mris preproc, mri
surf2surf using the measure volume and unsure of how to go about it since
the wiki page talks about thickness only. I would appreciate any help.

Best,
Sara
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Group Analysis: Comparing four groups

[Douglas N. Greve]

Yes, that is all correct. I only have a few comments. One is that 15mm 
is a lot of smoothing; this is not wrong, just more than the 5-10 that I 
usually use. Second, you might want to use permutation instead of MCZ; 
the threshold of 4 should make MCZ control the false positives 
adequately, but you might lose a lot of your activation.


On 10/21/2020 11:07 AM, Steve Petersen wrote:


External Email - Use Caution

Dear Freesurfer experts,

This is the first time I perform group analysis in Freesurfer. My aim 
is to compare the cortical thickness in four groups matched in age, 
sex and years of education using the Monte Carlo multiple comparisons 
correction. I tried to follow the Freesufer tutorials 
 
to perform this group analysis and I would be really grateful whether 
someone can verify that all steps are correct. For example, for the 
cortical thickness (smooth = 15 FWHM) of the left hemisphere, the four 
steps that I followed were:


STEP 1. Assemble the cached Data (mris_preproc) using the fsgd file

mris_preproc --fsgd STUDY_4groups.fsgd \
  --cache-in thickness.fwhm15.fsaverage \
  --target fsaverage \
  --hemi lh \
  --out lh_J4G_thickness.15.mgh \

STEP 2. Perform a GLM Analysis (mri_glmfit)

mri_glmfit \
--y lh_J4G_thickness.15.mgh \
--fsgd STUDY_4groups.fsgd \
--C *group.effect.mtx* \
--surf fsaverage lh \
--cortex \
--glmdir left_hemisphere_thickness_results\


STEP 3. Perform Monte Carlo simulation

mri_glmfit-sim \
  --glmdir left_hemisphere_thickness_results \
  --sim mc-z 1 4 mc-z.abs \
  --sim-sign abs --cwpvalthresh 0.05\
  --overwrite \


*QUESTIONS:*

1. Have I followed the steps to perform the analysis correctly or do 
you think I forgot some important flag?



2. Before test differences between two groups (eg. group1 > group 2 
with the vector 1 -1 0 0) I would like to test any group effect. For 
that purpose, I created the group.effect.mtx contrast file (see 
below), is correct?

1 -1 0 0
0 1 -1 0
0 0 1 -1


Any help would be appreciated.

Best regards,


Steve




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[Freesurfer] Group Analysis: Comparing four groups

[Steve Petersen]

External Email - Use Caution

Dear Freesurfer experts,

This is the first time I perform group analysis in Freesurfer. My aim is to
compare the cortical thickness in four groups matched in age, sex and years
of education using the Monte Carlo multiple comparisons correction. I tried
to follow the Freesufer tutorials
 to
perform this group analysis and I would be really grateful whether someone
can verify that all steps are correct. For example, for the cortical
thickness (smooth = 15 FWHM) of the left hemisphere, the four steps that I
followed were:

STEP 1. Assemble the cached Data (mris_preproc) using the fsgd file

mris_preproc --fsgd STUDY_4groups.fsgd \
  --cache-in thickness.fwhm15.fsaverage \
  --target fsaverage \
  --hemi lh \
  --out lh_J4G_thickness.15.mgh \

STEP 2. Perform a GLM Analysis (mri_glmfit)

mri_glmfit \
--y lh_J4G_thickness.15.mgh \
--fsgd STUDY_4groups.fsgd \
--C *group.effect.mtx* \
--surf fsaverage lh \
--cortex \
--glmdir left_hemisphere_thickness_results\


STEP 3. Perform Monte Carlo simulation

mri_glmfit-sim \
  --glmdir left_hemisphere_thickness_results \
  --sim mc-z 1 4 mc-z.abs \
  --sim-sign abs --cwpvalthresh 0.05\
  --overwrite \


*QUESTIONS:*

1. Have I followed the steps to perform the analysis correctly or do you
think I forgot some important flag?


2. Before test differences between two groups (eg. group1 > group 2 with
the vector 1 -1 0 0) I would like to test any group effect. For that
purpose, I created the group.effect.mtx contrast file (see below), is
correct?

1 -1 0 0
0 1 -1 0
0 0 1 -1


Any help would be appreciated.

Best regards,


Steve
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Re: [Freesurfer] Group Analysis Covariates

[Douglas N. Greve]

 21, 2020 10:32 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] question on partial volume correction

It will certainly do cortex. We do not have a segmentation for 
subarachnoid spaces. Or are you just talking about extra cerebral CSF? 
We do have a segmentation for xCSF, but it is not the most beautiful 
thing in the world. For WM, the GTM will give you a PVC corrected 
value for the entire lh and rh cerebral WM (and cerebellar) segments. 
Is that all you need?


On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect 
in the cortex, white matter and subarachnoid space. Is Freesurfer's 
partial volume correction working on all these areas or only the grey 
matter volume and surface? Is there a way to use gtmseg on the white 
matter and outside the pial surface?


Thanks a lot,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823



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Message: 3
Date: Thu, 21 May 2020 14:05:49 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] question on partial volume correction
To: 
Message-ID: <3904bd37-e3e4-4196-468c-586c4fcdb...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

You can try using --rbv. In theory, you can use mueller-gaertner
(--mgx), but I don't have it set up to look at WM or CSF. And be careful
because the extracerebral CSF segmentation is often not very good.

On 5/21/2020 1:07 PM, Barletta, Valeria wrote:
> Yes I need the lh and rh cerebral WM for sure, but not just the
> values, also an image.
> And I need also a corrected image for the extra cerebral CSF. How can
> I get that?
>
> Thank you very much,
>
> Valeria Barletta, MD
> Massachusetts General Hospital
> 149 13th Street, Charlestown MA 02129
> (617)-724-8823
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas N. Greve
> 
> *Sent:* Thursday, May 21, 2020 10:32 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* Re: [Freesurfer] question on partial volume correction
> It will certainly do cortex. We do not have a segmentation for
> subarachnoid spaces. Or are you just talking about extra cerebral CSF?
> We do have a segmentation for xCSF, but it is not the most beautiful
> thing in the world. For WM, the GTM will give you a PVC corrected
> value for the entire lh and rh cerebral WM (and cerebellar) segments.
> Is that all you need?
>
> On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
>> Dear Freesurfers,
>> We need to analyze PET data after correcting for partial volume
>> effect in the cortex, white matter and subarachnoid space. Is
>> Freesurfer's partial volume correction working on all these areas or
>> only the grey matter volume and surface? Is there a way to use gtmseg
>> on the white matter and outside the pial surface?
>>
>> Thanks a lot,
>>
>> Valeria Barletta, MD
>> Massachusetts General Hospital
>> 149 13th Street, Charlestown MA 02129
>> (617)-724-8823
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 4
Date: Thu, 21 May 2020 18:12:20 +
From: "Hua, Jessica" 
Subject: Re: [Freesurfer] Group Analysis Covariates
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID:


Content-Type: text/plain; charset="iso-2022-jp"

    External Email - Use Caution

I apologize for resending all of this info, but my email is acting up 
and every time I try to respond to the other email, my Outlook freezes.


Here is info from our thread. I modified it to include the analysis in 
which I found significant clusters (i.e., looking at thickness with 
only age and sex as covariates and not ICV):


After running the permutation and finding signi

Re: [Freesurfer] Group Analysis Covariates

[Hua, Jessica]

or xCSF, but it is not the most beautiful thing in the world. For 
WM, the GTM will give you a PVC corrected value for the entire lh and rh 
cerebral WM (and cerebellar) segments. Is that all you need?

On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
Dear Freesurfers,
We need to analyze PET data after correcting for partial volume effect in the 
cortex, white matter and subarachnoid space. Is Freesurfer's partial volume 
correction working on all these areas or only the grey matter volume and 
surface? Is there a way to use gtmseg on the white matter and outside the pial 
surface?

Thanks a lot,

Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
(617)-724-8823



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Message: 3
Date: Thu, 21 May 2020 14:05:49 -0400
From: "Douglas N. Greve" 
Subject: Re: [Freesurfer] question on partial volume correction
To: 
Message-ID: <3904bd37-e3e4-4196-468c-586c4fcdb...@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

You can try using --rbv. In theory, you can use mueller-gaertner
(--mgx), but I don't have it set up to look at WM or CSF. And be careful
because the extracerebral CSF segmentation is often not very good.

On 5/21/2020 1:07 PM, Barletta, Valeria wrote:
> Yes I need the lh and rh cerebral WM for sure, but not just the
> values, also an image.
> And I need also a corrected image for the extra cerebral CSF. How can
> I get that?
>
> Thank you very much,
>
> Valeria Barletta, MD
> Massachusetts General Hospital
> 149 13th Street, Charlestown MA 02129
> (617)-724-8823
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas N. Greve
> 
> *Sent:* Thursday, May 21, 2020 10:32 AM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* Re: [Freesurfer] question on partial volume correction
> It will certainly do cortex. We do not have a segmentation for
> subarachnoid spaces. Or are you just talking about extra cerebral CSF?
> We do have a segmentation for xCSF, but it is not the most beautiful
> thing in the world. For WM, the GTM will give you a PVC corrected
> value for the entire lh and rh cerebral WM (and cerebellar) segments.
> Is that all you need?
>
> On 5/19/2020 11:36 AM, Barletta, Valeria wrote:
>> Dear Freesurfers,
>> We need to analyze PET data after correcting for partial volume
>> effect in the cortex, white matter and subarachnoid space. Is
>> Freesurfer's partial volume correction working on all these areas or
>> only the grey matter volume and surface? Is there a way to use gtmseg
>> on the white matter and outside the pial surface?
>>
>> Thanks a lot,
>>
>> Valeria Barletta, MD
>> Massachusetts General Hospital
>> 149 13th Street, Charlestown MA 02129
>> (617)-724-8823
>>
>> ___
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>
>
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Message: 4
Date: Thu, 21 May 2020 18:12:20 +
From: "Hua, Jessica" 
Subject: Re: [Freesurfer] Group Analysis Covariates
To: "freesurfer@nmr.mgh.harvard.edu" 
Message-ID:



Content-Type: text/plain; charset="iso-2022-jp"

External Email - Use Caution

I apologize for resending all of this info, but my email is acting up and every 
time I try to respond to the other email, my Outlook freezes.

Here is info from our thread. I modified it to include the analysis in which I 
found significant clusters (i.e., looking at thickness with only age and sex as 
covariates and not ICV):

After running the permutation and finding significant clusters, I am trying to 
calculate the value for each participant for these significant clusters.

The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the 
adjusted values accounting for age and sex (this is a three group design).


The X matri

Re: [Freesurfer] Group Analysis Covariates

[Douglas N. Greve]

Typo
yhat = X(:,[1 2 3])*beta([1 2 3],:)

On 5/21/2020 2:12 PM, Hua, Jessica wrote:


External Email - Use Caution

I apologize for resending all of this info, but my email is acting up 
and every time I try to respond to the other email, my Outlook freezes.


Here is info from our thread. I modified it to include the analysis in 
which I found significant clusters (i.e., looking at thickness with 
only age and sex as covariates and not ICV):


After running the permutation and finding significant clusters, I am 
trying to calculate the value for each participant for these 
significant clusters.


The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to 
get the adjusted values accounting for age and sex (this is a three 
group design).


The X matrix was 240x12 (see attached file)

  * Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3
  * Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3
  * Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3
  * Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3
  * Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3
  * Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3
  * Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3
  * Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3
  * Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3 
Your code:

There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[1 2 3]*beta([1 2 3])

When running your code, below are the errors I got in Matlab. Do you 
know how I can fix the code?


>> X = load('Xg.dat');
>> y = load('perm.th30.abs.y.ocn.dat');
>> y = load('perm.th30.abs.y.ocn.dat');
>> beta = inv(X'*X)*X'*y;
>> yhat = X(:,[1 2 3]*beta([1 2 3])
 yhat = X(:,[1 2 3]*beta([1 2 3])
                                 ↑
Error: Invalid expression. When calling a function
or indexing a variable, use parentheses. Otherwise,
check for mismatched delimiters.

Did you mean:
>> yhat = X(:,[1 2 3]*beta([1 2 3]))
Error using  *
Incorrect dimensions for matrix multiplication.
Check that the number of columns in the first matrix
matches the number of rows in the second matrix. To
perform elementwise multiplication, use '.*'.

>> yhat = X(:,[1 2 3].*beta([1 2 3]))
Index in position 2 is invalid. Array indices must
be positive integers or logical values.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri

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Re: [Freesurfer] Group Analysis Covariates

[Hua, Jessica]

External Email - Use Caution

I apologize for resending all of this info, but my email is acting up and every 
time I try to respond to the other email, my Outlook freezes.

Here is info from our thread. I modified it to include the analysis in which I 
found significant clusters (i.e., looking at thickness with only age and sex as 
covariates and not ICV):

After running the permutation and finding significant clusters, I am trying to 
calculate the value for each participant for these significant clusters.

The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the 
adjusted values accounting for age and sex (this is a three group design).


The X matrix was 240x12 (see attached file)

  *   Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3
  *   Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3
  *   Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3
  *   Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3
  *   Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3
  *   Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3

Your code:
There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[1 2 3]*beta([1 2 3])

When running your code, below are the errors I got in Matlab. Do you know how I 
can fix the code?

>> X = load('Xg.dat');
>> y = load('perm.th30.abs.y.ocn.dat');
>> y = load('perm.th30.abs.y.ocn.dat');
>> beta = inv(X'*X)*X'*y;
>> yhat = X(:,[1 2 3]*beta([1 2 3])
 yhat = X(:,[1 2 3]*beta([1 2 3])
 ↑
Error: Invalid expression. When calling a function
or indexing a variable, use parentheses. Otherwise,
check for mismatched delimiters.

Did you mean:
>> yhat = X(:,[1 2 3]*beta([1 2 3]))
Error using  *
Incorrect dimensions for matrix multiplication.
Check that the number of columns in the first matrix
matches the number of rows in the second matrix. To
perform elementwise multiplication, use '.*'.

>> yhat = X(:,[1 2 3].*beta([1 2 3]))
Index in position 2 is invalid. Array indices must
be positive integers or logical values.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri


Xg.dat
Description: Xg.dat


perm.th30.abs.y.ocn.dat
Description: perm.th30.abs.y.ocn.dat


GroupComparison_AllMRI.AgeSex.xlsx
Description: GroupComparison_AllMRI.AgeSex.xlsx
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Re: [Freesurfer] Group Analysis Covariates

[Hua, Jessica]

External Email - Use Caution

Attached are the fsgd and Xg.dat files.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri


GroupComparison_AllMRI.AgeSexICV.fsgd
Description: GroupComparison_AllMRI.AgeSexICV.fsgd


Xg.dat
Description: Xg.dat
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Re: [Freesurfer] Group Analysis Covariates

[Hua, Jessica]

External Email - Use Caution

I was not sure how to modify the last line in your code in order to calculate 
adjusted values accounting for age, sex, and ICV for each participant (this is 
a three group design).

Your code:

There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[i j k ...]*beta([i j k ...])

where i j k ... indicate the factors you want keep in your data. Each
factor gets a column in the design matrix (and a beta). If you need help
figuring this out, send the fsgd file.



---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Re: [Freesurfer] Group Analysis Covariates

[Douglas Greve]

And what is your new question?

On 5/17/20 12:10 PM, Hua, Jessica wrote:


External Email - Use Caution

Sure, attached are the files again and here is our previous 
correspondence:


Original question:

After running the permutation and finding significant clusters, I am 
trying to calculate the value for each participant for these 
significant clusters.


The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to 
get the adjusted values accounting for age, sex, and ICV (this is a 
three group design).  What would be the best way of calculating that?


Your response:

There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[i j k ...]*beta([i j k ...])

where i j k ... indicate the factors you want keep in your data. Each
factor gets a column in the design matrix (and a beta). If you need help
figuring this out, send the fsgd file.


---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri

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Re: [Freesurfer] Group Analysis Covariates

[Hua, Jessica]

External Email - Use Caution

Sure, attached are the files again and here is our previous correspondence:

Original question:

After running the permutation and finding significant clusters, I am trying to 
calculate the value for each participant for these significant clusters.

The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the 
adjusted values accounting for age, sex, and ICV (this is a three group 
design).  What would be the best way of calculating that?

Your response:

There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[i j k ...]*beta([i j k ...])

where i j k ... indicate the factors you want keep in your data. Each
factor gets a column in the design matrix (and a beta). If you need help
figuring this out, send the fsgd file.


---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri


GroupComparison_AllMRI.AgeSexICV.fsgd
Description: GroupComparison_AllMRI.AgeSexICV.fsgd


Xg.dat
Description: Xg.dat
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Re: [Freesurfer] Group Analysis Covariates

[Douglas N. Greve]

Sorry, can you include previous correspondence so that I have context?

On 5/16/2020 1:55 PM, Hua, Jessica wrote:


External Email - Use Caution

Sure, attached is the FSGD file. In case helpful, I have also attached 
the Xg.dat file.


---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri

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Re: [Freesurfer] Group Analysis Covariates

[Hua, Jessica]

External Email - Use Caution

Sure, attached is the FSGD file. In case helpful, I have also attached the 
Xg.dat file.

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri


GroupComparison_AllMRI.AgeSexICV.fsgd
Description: GroupComparison_AllMRI.AgeSexICV.fsgd


Xg.dat
Description: Xg.dat
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Re: [Freesurfer] Group Analysis Covariates

[Douglas N. Greve]

There is not an easy way to do it, but you can do it in matlab
cd glmdir
X = load('Xg.dat');
y = load('perm.th30.abs.y.ocn.dat');
beta = inv(X'*X)*X'*y;
yhat = X(:,[i j k ...]*beta([i j k ...])

where i j k ... indicate the factors you want keep in your data. Each 
factor gets a column in the design matrix (and a beta). If you need help 
figuring this out, send the fsgd file.



On 5/15/2020 12:10 PM, Hua, Jessica wrote:


External Email - Use Caution

After running the permutation and finding significant clusters, I am 
trying to calculate the value for each participant for these 
significant clusters.


The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to 
get the adjusted values accounting for age, sex, and ICV.  What would 
be the best way of calculating that?


---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri

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Re: [Freesurfer] Group Analysis Covariates

[Hua, Jessica]

External Email - Use Caution

After running the permutation and finding significant clusters, I am trying to 
calculate the value for each participant for these significant clusters.

The perm.th30.abs.y.ocn.dat contain the raw values, and I am trying to get the 
adjusted values accounting for age, sex, and ICV.  What would be the best way 
of calculating that?

---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri
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Re: [Freesurfer] Group Analysis Covariates

[Douglas N. Greve]

That is how you would compute a partial model fit, though I'm not sure 
which part of the model you are trying to fit. In what you have, it will 
remove the main effect of group (but not interactions).


On 5/14/2020 1:30 PM, Hua, Jessica wrote:


External Email - Use Caution

Hi FreeSurfer Experts,
I am trying to extract or calculate the adjusted values for each participant in 
each cluster after accounting for covariates in my permutation analysis.
This is a 3 group analysis with 3 covariates (age, sex, and ICV).
After navigating to the glmdir folder of interest, I ran the following code:
X = load('Xg.dat');
The X matrix was 240x12 (see attached file)

  * Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3
  * Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3
  * Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3
  * Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3
  * Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3
  * Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3
  * Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3
  * Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3
  * Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3
  * Column 10: zICV for Group 1 and 0s for Group 2 and 0s for Group 3
  * Column 11: 0s for Group 1 and zICV for Group 2 and 0s for Group 3
  * Column 12: 0s for Group 1 and 0s for Group 2 and zICV for Group 3
beta = MRIread('beta.mgh');
betamat = fast_vol2mat(beta);
And I got stuck at this step: yhatmat = X(:,[i j k m n])*betamat([i j k m n],:);
I wasn't sure how to modify the code. Is this correct: yhatmat = X(:,[4 5 6 7 8 
9 10 11 12])*betamat([4 6 7 8 9 10 11 12],:);

Once I figure out the above step, I will finish with this code:
yhat = beta;

yhat.vol = fast_mat2vol(yhat,yhat.volsize);



---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri

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[Freesurfer] Group Analysis Covariates

[Hua, Jessica]

External Email - Use Caution

Hi FreeSurfer Experts,


I am trying to extract or calculate the adjusted values for each participant in 
each cluster after accounting for covariates in my permutation analysis.

This is a 3 group analysis with 3 covariates (age, sex, and ICV).


After navigating to the glmdir folder of interest, I ran the following code:


X = load('Xg.dat');


The X matrix was 240x12 (see attached file)

  *   Column 1: 1s for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 2: 0s for Group 1 and 1s for Group 2 and 0s for Group 3
  *   Column 3: 0s for Group 1 and 0s for Group 2 and 1s for Group 3
  *   Column 4: Age for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 5: 0s for Group 1 and Age for Group 2 and 0s for Group 3
  *   Column 6: 0s for Group 1 and 0s for Group 2 and Age for Group 3
  *   Column 7: Sex for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 8: 0s for Group 1 and Sex for Group 2 and 0s for Group 3
  *   Column 9: 0s for Group 1 and 0s for Group 2 and Sex for Group 3
  *   Column 10: zICV for Group 1 and 0s for Group 2 and 0s for Group 3
  *   Column 11: 0s for Group 1 and zICV for Group 2 and 0s for Group 3
  *   Column 12: 0s for Group 1 and 0s for Group 2 and zICV for Group 3

beta = MRIread('beta.mgh');


betamat = fast_vol2mat(beta);



And I got stuck at this step: yhatmat = X(:,[i j k m n])*betamat([i j k m n],:);

I wasn't sure how to modify the code. Is this correct: yhatmat = X(:,[4 5 6 7 8 
9 10 11 12])*betamat([4 6 7 8 9 10 11 12],:);


Once I figure out the above step, I will finish with this code:


yhat = beta;

yhat.vol = fast_mat2vol(yhat,yhat.volsize);



---

Jessica Hua, M.A.
Cognitive and Emotional Control Lab
Doctoral Candidate Clinical Psychology
University of Missouri


Xg.dat
Description: Xg.dat
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Re: [Freesurfer] group analysis of large data sets

[Douglas N. Greve]

I put one here that can go up to 80k
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit.80k


On 4/21/2020 3:15 PM, Inge Amlien wrote:


External Email - Use Caution

Hi Doug,
three years later and an order of magnitude more subjects.
Any chance you could raise the limit of maximum number of subjects 
further (>60K)?


Thanks a lot,
Inge
_
Inge Kasbohm Amlien, PhD
Center for Lifespan Changes in Brain and Cognition
University of Oslo, Norway


On 28 Mar 2017, at 18:24, Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>> wrote:


version 6 should be able to go up to 20,000


On 03/28/2017 11:45 AM, Wang, Xin wrote:

Thank you, Dr. Greve.
when I ran >2000 subjects in Version 5.3, I received this error 
message "##ERROR: gdfReadV1: the number of inputs in FSGD file 
exceeds the maximum allowed 2000##"
In your previous post about mri_glmfit, 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033151.html, 
I found

#define FSGDF_NCLASSES_MAX  128
#define FSGDF_NVARS_MAX 128
#define FSGDF_NINPUTS_MAX  2000
Are these the maximum? The mri_glmfit is written in C. Could you 
send me a version of mri_glmfit code without limits?

Thank you very much.

Xin

-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 27, 2017 1:47 PM
To: freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] group analysis of large data sets

I don't think there is a maximum size. You would do the big analysis 
the same way as the small.



On 03/26/2017 07:54 PM, Wang, Xin wrote:

Hello, FreeSurfer Group,

What is the maximal matrix size for glm_fit process?

How to use FreeSurfer for group analyses of more than 2000 subjects,
128 variables, and 128 Classes?

Thank you.

Xin



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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] group analysis of large data sets

[Inge Amlien]

External Email - Use Caution

Hi Doug,
three years later and an order of magnitude more subjects.
Any chance you could raise the limit of maximum number of subjects further 
(>60K)?

Thanks a lot,
Inge
_
Inge Kasbohm Amlien, PhD
Center for Lifespan Changes in Brain and Cognition
University of Oslo, Norway


On 28 Mar 2017, at 18:24, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

version 6 should be able to go up to 20,000


On 03/28/2017 11:45 AM, Wang, Xin wrote:
Thank you, Dr. Greve.
when I ran >2000 subjects in Version 5.3, I received this error message 
"##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum 
allowed 2000##"
In your previous post about mri_glmfit, 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033151.html,
 I found
#define FSGDF_NCLASSES_MAX  128
#define FSGDF_NVARS_MAX 128
#define FSGDF_NINPUTS_MAX  2000
Are these the maximum? The mri_glmfit is written in C. Could you send me a 
version of mri_glmfit code without limits?
Thank you very much.

Xin

-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 27, 2017 1:47 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] group analysis of large data sets

I don't think there is a maximum size. You would do the big analysis the same 
way as the small.


On 03/26/2017 07:54 PM, Wang, Xin wrote:
Hello, FreeSurfer Group,

What is the maximal matrix size for glm_fit process?

How to use FreeSurfer for group analyses of more than 2000 subjects,
128 variables, and 128 Classes?

Thank you.

Xin



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Fax: 617-726-7422

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Re: [Freesurfer] Group analysis

[Hengameh Marzbani]

External Email - Use Caution

I meant the latter.
Thank you very much for responding to my questions.

I have one more question: Can we do non-parametric approaches by Freesurfer?

On Sat, Mar 14, 2020 at 2:13 AM Douglas N. Greve 
wrote:

> Are you asking how to do subcortical analysis or are you asking how to
> account for subcortical analysis during correction for multiple
> corrections? For the latter, use --3spaces
>
> On 3/12/2020 2:03 PM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
> thank you for your detailed and helpful explanation.
>
> question 3: I mean just left and right. But what should I do if I want to
> consider subcortical as well as left and right?
>
> Best Regards
> Hengameh
>
> On Thu, Mar 12, 2020 at 12:07 AM Douglas N. Greve 
> wrote:
>
>>
>>
>> On 3/11/2020 4:21 PM, Hengameh Marzbani wrote:
>>
>> External Email - Use Caution
>>
>> Thank you for the quick response.
>>
>> question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). 
>> I can see the clusters by tksurfer. But, Can I have a text file included all 
>> clusters?
>>
>> You can, the easiest way is to run mri_glmfit-sim and it will give you a
>> list of clusters in a text file. If you set the cwp to 1, then it will give
>> you all the clusters. See the help.
>>
>> question 3: I want to do the analyse by considering the whole brain. Is 
>> correct to use --2spaces? and also I I want to visualize the results in both 
>> hemisphere simultaneously. is it possible by freeview?
>>
>> Whole brain meaning left, right, and subcort or just left and right? If
>> just left and right, then use --2spaces
>>
>> question 5: I can't understand what is the reason of using demean and 
>> normalize. Would you mind explaining to me? And when is it necessary to use 
>> them?
>>
>> Demeaning makes the design matrix better conditioned. But also if you are
>> looking at the difference in average thickness between two groups
>> regressing out, eg, age, then simply using age as a regressor will reduce
>> the efficiency of the estimation because the age itself will have a
>> non-zero mean, so the regression is left trying to figure out what part of
>> the thickness average is due to the group and what part is due to age.
>>
>> Thank you so much.
>>
>> Hengameh
>>
>>
>> On Tue, Mar 10, 2020 at 2:03 AM Douglas N. Greve 
>> wrote:
>>
>>>
>>>
>>> On 3/9/20 5:53 PM, Hengameh Marzbani wrote:
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Hello Freesurfer developers,
>>> > 1- I want to extract the uncorrected clusters from the uncorrected
>>> significance maps obtained from mri_glmfit for structural data (to
>>> illustrate cluster, size, location, and significance) like
>>> abs.sig.cluster.summary (summary of clusters (text))which is obtained from
>>> mri_glmfit-sim. Is there a way to do this?
>>> Set the clusterwise p-value thresh to 1 (--cwp 1)
>>> > 2- I don't see any clusters when I use cluster-based correction for
>>> multiple comparisons (for example mri_glmfit-sim \  --glmdir lh.Area.glmdir
>>> \ --sim mc-z 1 2 mc-z.abs\ --sim-sign abs --cache 4 neg \  --cwp
>>> 0.05\  --2spaces). How much is it significant if I report the uncorrected
>>> clusters?
>>> Usually, reveiewers won't let you report exclusivly uncorrected results.
>>> > 3- Are there new ways of looking at the whole brain together (not left
>>> and right hemisphere separately)by Qdec and FSGD?
>>> You can load both hemispheres into freeview, if that is what you mean
>>> > 4- How can I do fdr correction in mri_glmfit-sim? what flag should I
>>> use?
>>> You can't, use mri_fdr. Run with --help to get docs
>>> > 5- How can I demean and normalize the covariates when I use FSGD? what
>>> flag should I use?
>>> Add these lines in your FSGD file
>>> DeMeanFlag 1
>>> ReScaleFlag 1
>>> >
>>> > Thanks you in advance!
>>> > Best regards,
>>> > Hengameh
>>> >
>>> >
>>> >
>>> >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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>>
>>
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>
>
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>
>
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> 

Re: [Freesurfer] Group analysis

[Douglas N. Greve]

Are you asking how to do subcortical analysis or are you asking how to 
account for subcortical analysis during correction for multiple 
corrections? For the latter, use --3spaces


On 3/12/2020 2:03 PM, Hengameh Marzbani wrote:


External Email - Use Caution

thank you for your detailed and helpful explanation.

question 3: I mean just left and right. But what should I do if I want 
to consider subcortical as well as left and right?


Best Regards
Hengameh

On Thu, Mar 12, 2020 at 12:07 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:




On 3/11/2020 4:21 PM, Hengameh Marzbani wrote:


External Email - Use Caution

Thank you for the quick response.
question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). 
I can see the clusters by tksurfer. But, Can I have a text file included all 
clusters?

You can, the easiest way is to run mri_glmfit-sim and it will give
you a list of clusters in a text file. If you set the cwp to 1,
then it will give you all the clusters. See the help.

question 3: I want to do the analyse by considering the whole brain. Is 
correct to use --2spaces? and also I I want to visualize the results in both 
hemisphere simultaneously. is it possible by freeview?

Whole brain meaning left, right, and subcort or just left and
right? If just left and right, then use --2spaces

question 5: I can't understand what is the reason of using demean and 
normalize. Would you mind explaining to me? And when is it necessary to use 
them?

Demeaning makes the design matrix better conditioned. But also if
you are looking at the difference in average thickness between two
groups regressing out, eg, age, then simply using age as a
regressor will reduce the efficiency of the estimation because the
age itself will have a non-zero mean, so the regression is left
trying to figure out what part of the thickness average is due to
the group and what part is due to age.

Thank you so much.
Hengameh

On Tue, Mar 10, 2020 at 2:03 AM Douglas N. Greve
mailto:dgr...@mgh.harvard.edu>> wrote:



On 3/9/20 5:53 PM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer developers,
> 1- I want to extract the uncorrected clusters from the
uncorrected significance maps obtained from mri_glmfit for
structural data (to illustrate cluster, size, location, and
significance) like abs.sig.cluster.summary (summary of
clusters (text))which is obtained from mri_glmfit-sim. Is
there a way to do this?
Set the clusterwise p-value thresh to 1 (--cwp 1)
> 2- I don't see any clusters when I use cluster-based
correction for multiple comparisons (for example
mri_glmfit-sim \  --glmdir lh.Area.glmdir \ --sim mc-z 1
2 mc-z.abs\ --sim-sign abs --cache 4 neg \  --cwp  0.05\ 
--2spaces). How much is it significant if I report the
uncorrected clusters?
Usually, reveiewers won't let you report exclusivly
uncorrected results.
> 3- Are there new ways of looking at the whole brain
together (not left and right hemisphere separately)by Qdec
and FSGD?
You can load both hemispheres into freeview, if that is what
you mean
> 4- How can I do fdr correction in mri_glmfit-sim? what flag
should I use?
You can't, use mri_fdr. Run with --help to get docs
> 5- How can I demean and normalize the covariates when I use
FSGD? what flag should I use?
Add these lines in your FSGD file
DeMeanFlag 1
ReScaleFlag 1
>
> Thanks you in advance!
> Best regards,
> Hengameh
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Group analysis

[Hengameh Marzbani]

External Email - Use Caution

thank you for your detailed and helpful explanation.

question 3: I mean just left and right. But what should I do if I want to
consider subcortical as well as left and right?

Best Regards
Hengameh

On Thu, Mar 12, 2020 at 12:07 AM Douglas N. Greve 
wrote:

>
>
> On 3/11/2020 4:21 PM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
>
> Thank you for the quick response.
>
> question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). I 
> can see the clusters by tksurfer. But, Can I have a text file included all 
> clusters?
>
> You can, the easiest way is to run mri_glmfit-sim and it will give you a
> list of clusters in a text file. If you set the cwp to 1, then it will give
> you all the clusters. See the help.
>
> question 3: I want to do the analyse by considering the whole brain. Is 
> correct to use --2spaces? and also I I want to visualize the results in both 
> hemisphere simultaneously. is it possible by freeview?
>
> Whole brain meaning left, right, and subcort or just left and right? If
> just left and right, then use --2spaces
>
> question 5: I can't understand what is the reason of using demean and 
> normalize. Would you mind explaining to me? And when is it necessary to use 
> them?
>
> Demeaning makes the design matrix better conditioned. But also if you are
> looking at the difference in average thickness between two groups
> regressing out, eg, age, then simply using age as a regressor will reduce
> the efficiency of the estimation because the age itself will have a
> non-zero mean, so the regression is left trying to figure out what part of
> the thickness average is due to the group and what part is due to age.
>
> Thank you so much.
>
> Hengameh
>
>
> On Tue, Mar 10, 2020 at 2:03 AM Douglas N. Greve 
> wrote:
>
>>
>>
>> On 3/9/20 5:53 PM, Hengameh Marzbani wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hello Freesurfer developers,
>> > 1- I want to extract the uncorrected clusters from the uncorrected
>> significance maps obtained from mri_glmfit for structural data (to
>> illustrate cluster, size, location, and significance) like
>> abs.sig.cluster.summary (summary of clusters (text))which is obtained from
>> mri_glmfit-sim. Is there a way to do this?
>> Set the clusterwise p-value thresh to 1 (--cwp 1)
>> > 2- I don't see any clusters when I use cluster-based correction for
>> multiple comparisons (for example mri_glmfit-sim \  --glmdir lh.Area.glmdir
>> \ --sim mc-z 1 2 mc-z.abs\ --sim-sign abs --cache 4 neg \  --cwp
>> 0.05\  --2spaces). How much is it significant if I report the uncorrected
>> clusters?
>> Usually, reveiewers won't let you report exclusivly uncorrected results.
>> > 3- Are there new ways of looking at the whole brain together (not left
>> and right hemisphere separately)by Qdec and FSGD?
>> You can load both hemispheres into freeview, if that is what you mean
>> > 4- How can I do fdr correction in mri_glmfit-sim? what flag should I
>> use?
>> You can't, use mri_fdr. Run with --help to get docs
>> > 5- How can I demean and normalize the covariates when I use FSGD? what
>> flag should I use?
>> Add these lines in your FSGD file
>> DeMeanFlag 1
>> ReScaleFlag 1
>> >
>> > Thanks you in advance!
>> > Best regards,
>> > Hengameh
>> >
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Group analysis

[Douglas N. Greve]

On 3/11/2020 4:21 PM, Hengameh Marzbani wrote:


External Email - Use Caution

Thank you for the quick response.
question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). I 
can see the clusters by tksurfer. But, Can I have a text file included all 
clusters?
You can, the easiest way is to run mri_glmfit-sim and it will give you a 
list of clusters in a text file. If you set the cwp to 1, then it will 
give you all the clusters. See the help.

question 3: I want to do the analyse by considering the whole brain. Is correct 
to use --2spaces? and also I I want to visualize the results in both hemisphere 
simultaneously. is it possible by freeview?
Whole brain meaning left, right, and subcort or just left and right? If 
just left and right, then use --2spaces

question 5: I can't understand what is the reason of using demean and 
normalize. Would you mind explaining to me? And when is it necessary to use 
them?
Demeaning makes the design matrix better conditioned. But also if you 
are looking at the difference in average thickness between two groups 
regressing out, eg, age, then simply using age as a regressor will 
reduce the efficiency of the estimation because the age itself will have 
a non-zero mean, so the regression is left trying to figure out what 
part of the thickness average is due to the group and what part is due 
to age.

Thank you so much.
Hengameh

On Tue, Mar 10, 2020 at 2:03 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:




On 3/9/20 5:53 PM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer developers,
> 1- I want to extract the uncorrected clusters from the
uncorrected significance maps obtained from mri_glmfit for
structural data (to illustrate cluster, size, location, and
significance) like abs.sig.cluster.summary (summary of clusters
(text))which is obtained from mri_glmfit-sim. Is there a way to do
this?
Set the clusterwise p-value thresh to 1 (--cwp 1)
> 2- I don't see any clusters when I use cluster-based correction
for multiple comparisons (for example mri_glmfit-sim \  --glmdir
lh.Area.glmdir \ --sim mc-z 1 2 mc-z.abs\ --sim-sign abs
--cache 4 neg \  --cwp  0.05\ --2spaces). How much is it
significant if I report the uncorrected clusters?
Usually, reveiewers won't let you report exclusivly uncorrected
results.
> 3- Are there new ways of looking at the whole brain together
(not left and right hemisphere separately)by Qdec and FSGD?
You can load both hemispheres into freeview, if that is what you mean
> 4- How can I do fdr correction in mri_glmfit-sim? what flag
should I use?
You can't, use mri_fdr. Run with --help to get docs
> 5- How can I demean and normalize the covariates when I use
FSGD? what flag should I use?
Add these lines in your FSGD file
DeMeanFlag 1
ReScaleFlag 1
>
> Thanks you in advance!
> Best regards,
> Hengameh
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Group analysis

[Hengameh Marzbani]

External Email - Use Caution

Thank you for the quick response.


question 1: I need the results of mri-glmfit (before doing
mri-glmfit-sim). I can see the clusters by tksurfer. But, Can I have a
text file included all clusters?


question 3: I want to do the analyse by considering the whole brain.
Is correct to use --2spaces? and also I I want to visualize the
results in both hemisphere simultaneously. is it possible by freeview?


question 5: I can't understand what is the reason of using demean and
normalize. Would you mind explaining to me? And when is it necessary
to use them?


Thank you so much.

Hengameh


On Tue, Mar 10, 2020 at 2:03 AM Douglas N. Greve 
wrote:

>
>
> On 3/9/20 5:53 PM, Hengameh Marzbani wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer developers,
> > 1- I want to extract the uncorrected clusters from the uncorrected
> significance maps obtained from mri_glmfit for structural data (to
> illustrate cluster, size, location, and significance) like
> abs.sig.cluster.summary (summary of clusters (text))which is obtained from
> mri_glmfit-sim. Is there a way to do this?
> Set the clusterwise p-value thresh to 1 (--cwp 1)
> > 2- I don't see any clusters when I use cluster-based correction for
> multiple comparisons (for example mri_glmfit-sim \  --glmdir lh.Area.glmdir
> \ --sim mc-z 1 2 mc-z.abs\ --sim-sign abs --cache 4 neg \  --cwp
> 0.05\  --2spaces). How much is it significant if I report the uncorrected
> clusters?
> Usually, reveiewers won't let you report exclusivly uncorrected results.
> > 3- Are there new ways of looking at the whole brain together (not left
> and right hemisphere separately)by Qdec and FSGD?
> You can load both hemispheres into freeview, if that is what you mean
> > 4- How can I do fdr correction in mri_glmfit-sim? what flag should I use?
> You can't, use mri_fdr. Run with --help to get docs
> > 5- How can I demean and normalize the covariates when I use FSGD? what
> flag should I use?
> Add these lines in your FSGD file
> DeMeanFlag 1
> ReScaleFlag 1
> >
> > Thanks you in advance!
> > Best regards,
> > Hengameh
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Group analysis with qdec: qcache change this?

[Douglas N. Greve]

It will NOT affect any of the other files


On 3/10/2020 10:46 AM, Miguel Ángel Rivas Fernández wrote:


External Email - Use Caution

Dear freesurfer experts,

Before running group analysis in qdec is necessary run the qcache 
command over all subjects but, does this command change some 
segmentation file (eg. rh/lh Pial or white surface) or other 
importants file?
We would also like to perform external analysis using the output 
metrics obtained with the recon-all.  This is why we want to know if 
we can safely use this command without affecting any segmentation measure.


Thanks in advance


Best regards,

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[Freesurfer] Group analysis with qdec: qcache change this?

[Miguel Ángel Rivas Fernández]

External Email - Use Caution

Dear freesurfer experts,

Before running group analysis in qdec is necessary run the qcache command
over all subjects but, does this command change some segmentation file (eg.
rh/lh Pial or white surface) or other importants file?
We would also like to perform external analysis using the output metrics
obtained with the recon-all.  This is why we want to know if we can safely
use this command without affecting any segmentation measure.

Thanks in advance


Best regards,
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Re: [Freesurfer] Group analysis

[Douglas N. Greve]

On 3/9/20 5:53 PM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer developers,
> 1- I want to extract the uncorrected clusters from the uncorrected 
> significance maps obtained from mri_glmfit for structural data (to illustrate 
> cluster, size, location, and significance) like abs.sig.cluster.summary 
> (summary of clusters (text))which is obtained from mri_glmfit-sim. Is there a 
> way to do this?
Set the clusterwise p-value thresh to 1 (--cwp 1)
> 2- I don't see any clusters when I use cluster-based correction for multiple 
> comparisons (for example mri_glmfit-sim \  --glmdir lh.Area.glmdir \ --sim 
> mc-z 1 2 mc-z.abs\ --sim-sign abs --cache 4 neg \  --cwp  0.05\  
> --2spaces). How much is it significant if I report the uncorrected clusters?
Usually, reveiewers won't let you report exclusivly uncorrected results.
> 3- Are there new ways of looking at the whole brain together (not left and 
> right hemisphere separately)by Qdec and FSGD?
You can load both hemispheres into freeview, if that is what you mean
> 4- How can I do fdr correction in mri_glmfit-sim? what flag should I use?
You can't, use mri_fdr. Run with --help to get docs
> 5- How can I demean and normalize the covariates when I use FSGD? what flag 
> should I use?
Add these lines in your FSGD file
DeMeanFlag 1
ReScaleFlag 1
>
> Thanks you in advance!
> Best regards,
> Hengameh
>
>
>
>
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[Freesurfer] Group analysis

[Hengameh Marzbani]

External Email - Use Caution

Hello Freesurfer developers,


1- I want to extract the uncorrected clusters from the uncorrected
significance maps obtained from mri_glmfit for structural data (to
illustrate cluster, size, location, and significance) like
abs.sig.cluster.summary (summary of clusters (text))which is obtained
from mri_glmfit-sim. Is there a way to do this?


2- I don't see any clusters when I use cluster-based correction for
multiple comparisons (for example mri_glmfit-sim \  --glmdir
lh.Area.glmdir \ --sim mc-z 1 2 mc-z.abs\ --sim-sign abs --cache 4
neg \  --cwp  0.05\  --2spaces). How much is it significant if I
report the uncorrected clusters?


3- Are there new ways of looking at the whole brain together (not left
and right hemisphere separately)by Qdec and FSGD?


4- How can I do fdr correction in mri_glmfit-sim? what flag should I use?


5- How can I demean and normalize the covariates when I use FSGD? what flag
should I use?

Thanks you in advance!
Best regards,
Hengameh
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Re: [Freesurfer] group analysis for same group in 2 conditions

[Douglas N. Greve]

What quantity do you want to compare across subjects/goggle condition? 
Sorry for the delay, I have not worked much with the retinotopy code in 
a while and don't have it at my fingertips



On 3/2/2020 9:08 AM, Marco Ninghetto wrote:


External Email - Use Caution

Since that each subject undergoes to both conditions and functional 
images are in 2 different folders, I modify my folder structure and 
put functional folders together. It means that now I have a main 
functional folder (pRFs_functionals) in which I have all subjects two 
times named differently (eg: SUBJ06YG and SUBJ06NG, where YG means 
with goggles condition and NG means without goggles condition). 
Something like below:

image.png
All the subjects have one structural image in a folder named 
"fs_output". Now that all functionals are together, my question is how 
to create the FSGD file. At this moment FSGD looks like this:

image.png
Each subject has his own structural data saved in a folder called 
"sub-xx", inside the main folder from "recon-all". So, my doubt is how 
to name subjects inside the FSGD in such a way that FREESURFER would 
know it has to compare the same subject two times in two different 
conditions.

Command is:

mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi
?h --out ?h.out.retinotopy

Thank you for your effort in solving this matter,
Marco

On Fri, 28 Feb 2020 at 23:17, Marco Ninghetto 
mailto:m.ninghe...@nencki.edu.pl>> wrote:


Thanks for your support. Here my "mkanalysis-sess" command:

mkanalysis-sess -a rtopy.self.?h.ng -surface self ?h
-paradigm rtopy.par -retinotopy 41 -TR 2.5 -fsd bold -fwhm
5 -per-run


I run this command for both no goggles condition
(rtopy.self.?h.ng) and for yes goggles (rtopy.self.?h.yg).
The functional data were acquired using rotating wedge 45deg
counter-clockwise and expanding ring (out) stimuli. One cycle
lasted 41sec, each stimulus had 6 cycles.


On Fri, 28 Feb 2020, 22:24 Douglas N. Greve,
mailto:dgr...@mgh.harvard.edu>> wrote:

What quantity from the retinotopy analysis do you want to
compare across subjects? Eg, the phase? Can you send your
mkanalysis-sess command?

On 2/28/2020 8:17 AM, Marco Ninghetto wrote:


External Email - Use Caution

Dear experts,
I'm performing a study on visual pathways, in which each
participant undergoes to 2 different conditions. One in
normal sight (NG, i.e.: No Goggles) and second in narrowed
sight using special goggles (YG, i.e.: Yes Goggles). I'd like
to compare the results between these two conditions
(basically, subject A, B, C in cond1 versus subject A, B, C
in cond2).

I created the FSGD file (attached as "RetinotopyStudy" file)
and the contrast matrices, organised as:

1 -1 , named "YG-NG.mtx"
-1 1,  named "NG-YG.mtx"

In this FSGD sample file, I reported only subjects from 7 to 12.
My folders are organised as follows:

main >> recon_output  >> sub-yy (X folders for X
subjects)
>> Contrasts (with contrast files)
>> FSGD (with FSGD files)
>> fsaverage (subjects template created during
recon-all -qcache)
        >> pRF_function >> analNG (inside, there are
the functionals for each subject in NG condition)
>> analYG  (inside, there are the functionals for
each subject in YG condition) 



Once I used the pipeline for the retinotopy analysis
and
I have results for each participant, and now I'd like to make
2nd lev analysis. So the idea would be, as you probably
already got it, condition Yes Goggles versus condition No
Goggles. I use the command:

mris_preproc --fsgd RetinotopyStudy --target
fsaverage --hemi ?h --out outputname.mgh


But I'm not sure it would calculate in the right way.
The question is: how would I organise the FSGD file or
folders in such a way that FREESURFER would know that it has
to compare results from the same subjects but from two
different folders (analNG vs analYG)?

Hoping that's clear, I really look forward to hear from you soon.
Thank you for your time,
Marco

-- 
---

Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland

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Re: [Freesurfer] group analysis for same group in 2 conditions

[Marco Ninghetto]

External Email - Use Caution

Since that each subject undergoes to both conditions and functional images
are in 2 different folders, I modify my folder structure and put functional
folders together. It means that now I have a main functional folder
(pRFs_functionals) in which I have all subjects two times named differently
(eg: SUBJ06YG and SUBJ06NG, where YG means with goggles condition and NG
means without goggles condition). Something like below:
[image: image.png]
All the subjects have one structural image in a folder named "fs_output".
Now that all functionals are together, my question is how to create the
FSGD file. At this moment FSGD looks like this:
[image: image.png]
Each subject has his own structural data saved in a folder called "sub-xx",
inside the main folder from "recon-all". So, my doubt is how to name
subjects inside the FSGD in such a way that FREESURFER would know it has to
compare the same subject two times in two different conditions.
Command is:

mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi ?h --out
> ?h.out.retinotopy



Thank you for your effort in solving this matter,
Marco

On Fri, 28 Feb 2020 at 23:17, Marco Ninghetto 
wrote:

> Thanks for your support. Here my "mkanalysis-sess" command:
>
> mkanalysis-sess -a rtopy.self.?h.ng -surface self ?h -paradigm rtopy.par
>> -retinotopy 41 -TR 2.5 -fsd bold -fwhm 5 -per-run
>
>
> I run this command for both no goggles condition (rtopy.self.?h.ng) and for
> yes goggles (rtopy.self.?h.yg).
> The functional data were acquired using rotating wedge 45deg
> counter-clockwise and expanding ring (out) stimuli. One cycle lasted 41sec,
> each stimulus had 6 cycles.
>
>
> On Fri, 28 Feb 2020, 22:24 Douglas N. Greve, 
> wrote:
>
>> What quantity from the retinotopy analysis do you want to compare across
>> subjects? Eg, the phase? Can you send your mkanalysis-sess command?
>>
>> On 2/28/2020 8:17 AM, Marco Ninghetto wrote:
>>
>> External Email - Use Caution
>> Dear experts,
>> I'm performing a study on visual pathways, in which each participant
>> undergoes to 2 different conditions. One in normal sight (NG, i.e.: No
>> Goggles) and second in narrowed sight using special goggles (YG, i.e.: Yes
>> Goggles). I'd like to compare the results between these two conditions
>> (basically, subject A, B, C in cond1 versus subject A, B, C in cond2).
>>
>> I created the FSGD file (attached as "RetinotopyStudy" file) and the
>> contrast matrices, organised as:
>>
>> 1 -1 , named "YG-NG.mtx"
>>> -1 1,  named "NG-YG.mtx"
>>
>>
>> In this FSGD sample file, I reported only subjects from 7 to 12.
>> My folders are organised as follows:
>>
>> main >> recon_output  >> sub-yy (X folders for X subjects)
>>> >> Contrasts (with contrast files)
>>> >> FSGD (with FSGD files)
>>> >> fsaverage (subjects template
>>> created during recon-all -qcache)
>>> >> pRF_function >> analNG (inside, there are the functionals for
>>> each subject in NG condition)
>>> >> analYG  (inside, there are the
>>> functionals for each subject in YG condition)
>>
>>
>>
>> Once I used the pipeline for the retinotopy analysis
>> and I
>> have results for each participant, and now I'd like to make 2nd lev
>> analysis. So the idea would be, as you probably already got it, condition
>> Yes Goggles versus condition No Goggles. I use the command:
>>
>> mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi ?h --out
>>> outputname.mgh
>>
>>
>> But I'm not sure it would calculate in the right way.
>> The question is: how would I organise the FSGD file or folders in such a
>> way that FREESURFER would know that it has to compare results from the same
>> subjects but from two different folders (analNG vs analYG)?
>>
>> Hoping that's clear, I really look forward to hear from you soon.
>> Thank you for your time,
>> Marco
>>
>> --
>> ---
>> Marco Ninghetto, PhD candidate
>> Laboratory of Neuroplasticity
>> Nencki Institute of Experimental Biology
>> Polish Academy of Sciences
>> 3 Pasteur Street, 02-093 Warsaw, Poland
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
---
Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland
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Re: [Freesurfer] group analysis for same group in 2 conditions

[Marco Ninghetto]

External Email - Use Caution

Thanks for your support. Here my "mkanalysis-sess" command:

mkanalysis-sess -a rtopy.self.?h.ng -surface self ?h -paradigm rtopy.par
> -retinotopy 41 -TR 2.5 -fsd bold -fwhm 5 -per-run


I run this command for both no goggles condition (rtopy.self.?h.ng) and for
yes goggles (rtopy.self.?h.yg).
The functional data were acquired using rotating wedge 45deg
counter-clockwise and expanding ring (out) stimuli. One cycle lasted 41sec,
each stimulus had 6 cycles.


On Fri, 28 Feb 2020, 22:24 Douglas N. Greve,  wrote:

> What quantity from the retinotopy analysis do you want to compare across
> subjects? Eg, the phase? Can you send your mkanalysis-sess command?
>
> On 2/28/2020 8:17 AM, Marco Ninghetto wrote:
>
> External Email - Use Caution
> Dear experts,
> I'm performing a study on visual pathways, in which each participant
> undergoes to 2 different conditions. One in normal sight (NG, i.e.: No
> Goggles) and second in narrowed sight using special goggles (YG, i.e.: Yes
> Goggles). I'd like to compare the results between these two conditions
> (basically, subject A, B, C in cond1 versus subject A, B, C in cond2).
>
> I created the FSGD file (attached as "RetinotopyStudy" file) and the
> contrast matrices, organised as:
>
> 1 -1 , named "YG-NG.mtx"
>> -1 1,  named "NG-YG.mtx"
>
>
> In this FSGD sample file, I reported only subjects from 7 to 12.
> My folders are organised as follows:
>
> main >> recon_output  >> sub-yy (X folders for X subjects)
>> >> Contrasts (with contrast files)
>> >> FSGD (with FSGD files)
>> >> fsaverage (subjects template
>> created during recon-all -qcache)
>> >> pRF_function >> analNG (inside, there are the functionals for
>> each subject in NG condition)
>> >> analYG  (inside, there are the
>> functionals for each subject in YG condition)
>
>
>
> Once I used the pipeline for the retinotopy analysis
> and I
> have results for each participant, and now I'd like to make 2nd lev
> analysis. So the idea would be, as you probably already got it, condition
> Yes Goggles versus condition No Goggles. I use the command:
>
> mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi ?h --out
>> outputname.mgh
>
>
> But I'm not sure it would calculate in the right way.
> The question is: how would I organise the FSGD file or folders in such a
> way that FREESURFER would know that it has to compare results from the same
> subjects but from two different folders (analNG vs analYG)?
>
> Hoping that's clear, I really look forward to hear from you soon.
> Thank you for your time,
> Marco
>
> --
> ---
> Marco Ninghetto, PhD candidate
> Laboratory of Neuroplasticity
> Nencki Institute of Experimental Biology
> Polish Academy of Sciences
> 3 Pasteur Street, 02-093 Warsaw, Poland
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] group analysis for same group in 2 conditions

[Douglas N. Greve]

What quantity from the retinotopy analysis do you want to compare across 
subjects? Eg, the phase? Can you send your mkanalysis-sess command?


On 2/28/2020 8:17 AM, Marco Ninghetto wrote:


External Email - Use Caution

Dear experts,
I'm performing a study on visual pathways, in which each participant 
undergoes to 2 different conditions. One in normal sight (NG, i.e.: No 
Goggles) and second in narrowed sight using special goggles (YG, i.e.: 
Yes Goggles). I'd like to compare the results between these two 
conditions (basically, subject A, B, C in cond1 versus subject A, B, C 
in cond2).


I created the FSGD file (attached as "RetinotopyStudy" file) and the 
contrast matrices, organised as:


1 -1 , named "YG-NG.mtx"
-1 1,  named "NG-YG.mtx"

In this FSGD sample file, I reported only subjects from 7 to 12.
My folders are organised as follows:

main >> recon_output  >> sub-yy (X folders for X subjects)
                                    >> Contrasts (with
contrast files)
                                    >> FSGD (with FSGD files)
                                    >> fsaverage (subjects
template created during recon-all -qcache)
        >> pRF_function >> analNG (inside, there are the
functionals for each subject in NG condition)
                                    >> analYG (inside, there
are the functionals for each subject in YG condition) 



Once I used the pipeline for the retinotopy analysis 
and I 
have results for each participant, and now I'd like to make 2nd lev 
analysis. So the idea would be, as you probably already got it, 
condition Yes Goggles versus condition No Goggles. I use the command:


mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi
?h --out outputname.mgh


But I'm not sure it would calculate in the right way.
The question is: how would I organise the FSGD file or folders in such 
a way that FREESURFER would know that it has to compare results from 
the same subjects but from two different folders (analNG vs analYG)?


Hoping that's clear, I really look forward to hear from you soon.
Thank you for your time,
Marco

--
---
Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland

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[Freesurfer] group analysis for same group in 2 conditions

[Marco Ninghetto]

External Email - Use Caution

Dear experts,
I'm performing a study on visual pathways, in which each participant
undergoes to 2 different conditions. One in normal sight (NG, i.e.: No
Goggles) and second in narrowed sight using special goggles (YG, i.e.: Yes
Goggles). I'd like to compare the results between these two conditions
(basically, subject A, B, C in cond1 versus subject A, B, C in cond2).

I created the FSGD file (attached as "RetinotopyStudy" file) and the
contrast matrices, organised as:

1 -1 , named "YG-NG.mtx"
> -1 1,  named "NG-YG.mtx"


In this FSGD sample file, I reported only subjects from 7 to 12.
My folders are organised as follows:

main >> recon_output  >> sub-yy (X folders for X subjects)
> >> Contrasts (with contrast files)
> >> FSGD (with FSGD files)
> >> fsaverage (subjects template
> created during recon-all -qcache)
> >> pRF_function >> analNG (inside, there are the functionals for
> each subject in NG condition)
> >> analYG  (inside, there are the
> functionals for each subject in YG condition)



Once I used the pipeline for the retinotopy analysis
and I have
results for each participant, and now I'd like to make 2nd lev analysis. So
the idea would be, as you probably already got it, condition Yes Goggles
versus condition No Goggles. I use the command:

mris_preproc --fsgd RetinotopyStudy --target fsaverage --hemi ?h --out
> outputname.mgh


But I'm not sure it would calculate in the right way.
The question is: how would I organise the FSGD file or folders in such a
way that FREESURFER would know that it has to compare results from the same
subjects but from two different folders (analNG vs analYG)?

Hoping that's clear, I really look forward to hear from you soon.
Thank you for your time,
Marco

-- 
---
Marco Ninghetto, PhD candidate
Laboratory of Neuroplasticity
Nencki Institute of Experimental Biology
Polish Academy of Sciences
3 Pasteur Street, 02-093 Warsaw, Poland
GroupDescriptorFile 1   
Title RetinotopyStudy   
Class YG
Class NG
Input   sub-07  YG
Input   sub-08  YG
Input   sub-09  YG
Input   sub-10  YG
Input   sub-11  YG
Input   sub-12  YG
Input   sub-07  NG
Input   sub-08  NG
Input   sub-09  NG
Input   sub-10  NG
Input   sub-11  NG
Input   sub-12  NG
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Re: [Freesurfer] Group analysis with gray matter volume in FS 6.0

[Greve, Douglas N.,Ph.D.]

When you say "gray matter volume", does it mean you are trying to do a 
VBM-style analysis? You can't do VBM with FS. You can do an analysis of 
cortical GM volume in a similar way. When you run mris_preproc, specify 
"volume" as the --meas

On 12/12/19 12:58 PM, Marisa Cathryn Ross wrote:
>
> External Email - Use Caution
>
> Hello,
>
> Thanks in advance for your patience with what is probably a very basic 
> question!
>
> We would like to run a group analysis with gray matter volume at the 
> voxel level following manual edits, and we are unsure which .mgz file 
> is the proper output to use as the final output from manual edits. We 
> do not have brain.finalsurfs.manedit.mgz files. Which subject file is 
> the recommended output to use for a whole-brain voxel level group 
> analysis after manual edits? I have included a screenshot of an 
> example subject’s /mri directory below.
>
> A screenshot of text Description automatically generated
>
> Thank you,
>
> Marisa Ross
>
> -- 
>
> /Marisa C. Ross, MPA/
>
> PhD Candidate
>
>
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Re: [Freesurfer] Group analysis

[Greve, Douglas N.,Ph.D.]

On 3/4/19 10:11 AM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> I want to do group analysis on four groups and use the volume values 
> in aseg,stats.
> 1- Is it correct that each subcortical segmentation is based on a 
> "volumetric segmentation atlas" created by Freesurfer?
Yes
> 2- Are the volume values expressed in the space of this atlas?
No, they are in native space units.
> 3- Can I compare these absolute values between 4 groups ?
Yes.
> 4- Should I apply correction to the volume measures by eTIV (also 
> called ICV)?
Probably so, but you should know better than us
>
>
> Thanks you in advance!
>
> Best regards,
> Hengameh
>
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[Freesurfer] Group analysis

[Hengameh Marzbani]

External Email - Use Caution

Hi Freesurfers,

I want to do group analysis on four groups and use the volume values in
aseg,stats.
1- Is it correct that each subcortical segmentation is based on a
"volumetric segmentation atlas" created by Freesurfer?
2- Are the volume values expressed in the space of this atlas?
3- Can I compare these absolute values between 4 groups ?
4- Should I apply correction to the volume measures by eTIV (also called
ICV)?


Thanks you in advance!

Best regards,
Hengameh
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Re: [Freesurfer] Group Analysis Covariates

[Douglas Greve]

sorry for the delay. There is not a super easy way to do this, but it is 
possible in matlab. cd into the glmdir folder and start matlab, then


X = load('Xg.dat');

beta = MRIread('beta.mgh');

betamat = fast_vol2mat(beta);

yhatmat = X(:,[i j k m n])*betamat([i j k m n],:);

yhat = beta;

yhat.vol = fast_mat2vol(yhat,yhat.volsize);

MRIwrite(yhat,'yhat.ijkmn.mgh');


The key here is that you need to select the covariates (i j k m n) that 
you want to include. Each one will form a column in the design matrix 
and will have an element in the beta. By selecting the components you 
want, you exclude the ones you don't want. this simple formulation won't 
work if a given component spans both a factor of interest and a nuisance 
factor (eg, Male-AD when you want remove the effects of gender). But 
there is a way around this too. let me know.





On 6/24/18 9:58 AM, Hua, Jessica wrote:



Hi FreeSurfer experts,


Just bringing this question back up to the top: I analyzed my data 
following the guidelines on the FreeSurfer Tutorial/Group Analysis 
page . I am trying to plot the adjusted values (covariates: age, sex, 
and ICV) for the significant clusters for each of my participants.


Is there a way to extract or calculate the adjusted values for each 
participant in each cluster after accounting for covariates (age, sex, 
and ICV)?



Best,


Jessica





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*Subject:* Freesurfer Digest, Vol 172, Issue 36
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   2. Using grad_unwarp (James Gullickson)


--

Message: 1
Date: Fri, 22 Jun 2018 11:37:44 -0500
From: David S Lee 
Subject: [Freesurfer] FreeSurfer Manual Edit Sequence
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

    External Email - Use Caution

Hello Experts,

When performing manual edits on brain masks, white matter, and gray 
matter,

do I have to strictly follow the sequences(process stages) listed here
?

For instance, the link suggests that "autorecon2-pial is used after 
editing

brain volume *after running -autorecon2".

In other words, is it okay to perform "autorecon2-pial" before
"autorecon2-wm"?

Thank you for your time,
--
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Message: 2
Date: Fri, 22 Jun 2018 13:55:53 -0500
From: James Gullickson 
Subject: [Freesurfer] Using grad_unwarp
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="utf-8"

    External Email - Use Caution

All,

I am interested in using grad_unwarp. I have been reading up on the
documentation a bit and from what I understand not all the necessary files
are distributed with the public version of Freesurfer, due to proprietary
information in the tables. However, there is a script called 
grad_unwarp in

 my $FREESURFER_HOME/bin directory. I have access to the .grad files
necessary for my project, so I was planning to just piece together the
environment manually. Based on: https://surfer.nmr.mgh 
.

harvard.edu/fswiki/GradUnwarp there are a few pieces I'm missing:

   - create_displacement_tables script
   - grad_unwarp_converter.pl script
   -  matlab files

Is there somewhere I can locate these missing scripts/files?

Thanks,

James
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Re: [Freesurfer] Group Analysis Covariates

[Hua, Jessica]

External Email - Use Caution

Hi FreeSurfer experts,


Just bringing this question back up to the top: I analyzed my data following 
the guidelines on the FreeSurfer Tutorial/Group Analysis page . I am trying to 
plot the adjusted values (covariates: age, sex, and ICV) for the significant 
clusters for each of my participants.


Is there a way to extract or calculate the adjusted values for each participant 
in each cluster after accounting for covariates (age, sex, and ICV)?


Best,


Jessica




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu 
Sent: Saturday, June 23, 2018 11:00 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 172, Issue 36

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Today's Topics:

   1. FreeSurfer Manual Edit Sequence (David S Lee)
   2. Using grad_unwarp (James Gullickson)


--

Message: 1
Date: Fri, 22 Jun 2018 11:37:44 -0500
From: David S Lee 
Subject: [Freesurfer] FreeSurfer Manual Edit Sequence
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:

Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

Hello Experts,

When performing manual edits on brain masks, white matter, and gray matter,
do I have to strictly follow the sequences(process stages) listed here
?

For instance, the link suggests that "autorecon2-pial is used after editing
brain volume *after running -autorecon2".

In other words, is it okay to perform "autorecon2-pial" before
"autorecon2-wm"?

Thank you for your time,
--
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Message: 2
Date: Fri, 22 Jun 2018 13:55:53 -0500
From: James Gullickson 
Subject: [Freesurfer] Using grad_unwarp
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="utf-8"

External Email - Use Caution

All,

I am interested in using grad_unwarp. I have been reading up on the
documentation a bit and from what I understand not all the necessary files
are distributed with the public version of Freesurfer, due to proprietary
information in the tables. However, there is a script called grad_unwarp in
 my $FREESURFER_HOME/bin directory. I have access to the .grad files
necessary for my project, so I was planning to just piece together the
environment manually. Based on:  https://surfer.nmr.mgh.
harvard.edu/fswiki/GradUnwarp there are a few pieces I'm missing:

   - create_displacement_tables script
   - grad_unwarp_converter.pl script
   -  matlab files

Is there somewhere I can locate these missing scripts/files?

Thanks,

James
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Re: [Freesurfer] Group Analysis Covariates

[Douglas N. Greve]

The value in the ocn.dat file totally depends on what you used as input 
(--y) to mri_glmfit. If you used thickness, then it is thickness. That 
mri_segstats command is almost correct. You will need to add 
--accumulate so that it gives you the total volume rather than the average


On 06/13/2018 12:47 PM, Hua, Jessica wrote:
>
> External Email - Use Caution
>
> Thank you for your response!
>
>
> Just to clarify: if my input is volume, does the 
> cache.th20.abs.sig.y.ocn.dat contain the average unadjusted volume 
> values for each participant in each significant cluster?
>
>
> Since the file I just mentioned contains the average values, I used 
> mri_segstats to calculate total volume for the cluster.
>
>
> mri_segstats --i   --seg 
> cache.th20.abs.sig.ocn.mgh --excludeid 0 --sumwf ClusterVolumeValues.dat
>
> However, this just calculates the sum of the unadjusted values in the 
> cluster. I guess my main question is, is there a way to extract or 
> calculate the adjusted values for each participant in each cluster 
> after accounting for covariates (age, sex, and ICV)?
>
>
> ---
>
> Jessica
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of 
> freesurfer-requ...@nmr.mgh.harvard.edu 
> 
> *Sent:* Wednesday, June 13, 2018 11:00 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Freesurfer Digest, Vol 172, Issue 21
> Send Freesurfer mailing list submissions to
>     freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
>     freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
>     freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
>    1. Re: crypt_gkey = (null) (Dicamillo, Robert)
>    2. tractstats2table - all tracts for multiple subjects
>   (Alexopoulos, Dimitrios)
>    3. Re: tractstats2table - all tracts for multiple subjects
>   (Yendiki, Anastasia)
>    4. dwi.ecclog file (Daumail, Loic Jean)
>    5. Re: dwi.ecclog file (Yendiki, Anastasia)
>    6. Re: tractstats2table - all tracts for multiple subjects
>   (Alexopoulos, Dimitrios)
>    7. Re: Missing Control Points and QATools (Matthew Peverill)
>    8. Re: Missing Control Points and QATools (Bruce Fischl)
>    9. Re: Extract the entorhinal cortex as a mask (Erik O'Hanlon)
>   10. PREDOCTORAL POSITION at King's College London
>   (Walter Hugo Lopez Pinaya)
>   11. Re: Extract the entorhinal cortex as a mask (Bruce Fischl)
>   12. Re: "WARNING: Image geometries differ across time" upon
>   running base step of longitudinal pipeline (Tudor Popescu)
>   13. Re: dwi.ecclog file (Daumail, Loic Jean)
>   14. Re: Running qcache on old FS data (Douglas N. Greve)
>   15. Re: Group Analysis Covariates (Douglas N. Greve)
>   16. Re: Error during QDEC (Douglas N. Greve)
>
>
> --
>
> Message: 1
> Date: Tue, 12 Jun 2018 19:52:52 +
> From: "Dicamillo, Robert" 
> Subject: Re: [Freesurfer] crypt_gkey = (null)
> To: Freesurfer support list 
> Message-ID: <5024346d-6c53-4e0f-8189-faae089d2...@mgh.harvard.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hello Aaron,
>
> The build timestamp from the output below shows mri_convert is from 
> 8/2014.  When I look at the build timestamp on our stable 5.3 version 
> of mri_convert I see it is from 5/2013.  So the version that you 
> listed is about 1 year newer than the 5.3 release I can see. It is 
> possible that someone downloaded a daily/dev build of freesurfer at 
> that time.
>
> You might want to consider running the latest 6.0 release of 
> Freesurfer (released in January 2017), which should be fine on CentOS 
> 7.  It can be downloaded from, 
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
> I also suggest that you start out in a default/clean shell,  set 
> FREESURFER_HOME, and then source the setup script for linux,  You can 
> see the instructions on that same web page under ?Setup and 
> Configuration?. The setup steps should work for version 5 or 6.
>
> - rob
>
> On Jun 12, 2018, at 2:43 PM, Aaron Tanenbaum 
> mailto:aaron.b.tanenb...@gmail.com>> wrote:
>
>
>     External Email - Use Caution
>
> I checked my system is not encrypted. I had someone else run the 
> command on the same machine. It worked for them. So I changed my BASH 
> environment to a default environment. I still get the same error.
>
> I tried this again but with a different FreeSurfer 5.3. turns out the 
> one I was using has been altered version of FreeSurfer.  I do not know 
> how it was altered. It worked. so it has to do with the altered 
> FreeSurfer.
> I ran the command 

Re: [Freesurfer] Group Analysis Covariates

[Douglas N. Greve]

On 06/11/2018 11:07 PM, Hua, Jessica wrote:
>
>
> Dear Freesurfer Experts:
>
>
> I analyzed my data following the guidelines on the FSL Tutorial/Group 
> Analysis page . I am trying to plot the adjusted values (covariates: 
> age, sex, and ICV) for the significant clusters for each of my 
> participants.
>
I assume you mean FreeSurfer, not FSL?
>
>
> I set up the contrast to test group differences. So testing whether 
> there is a difference between groups regressing out the effects of 
> sex, age, and ICV. Contrasts created were  [1 -1 0 0 0 0 0 0] and [-1 
> 1 0 0 0 0 0 0].
>
>
> I then extracted values from this file 
> (cache.th20.abs.sig.y.ocn.dat; i.e., the average value of each subject 
> in each cluster) into my dataset. I believe these are the unadjusted 
> values, correct?
>
These are the average thickness data (assuming you are using thickness 
as input --y)
>
> I calculated total volume and total surface area by multiplying these 
> values by the total number of vertices in each cluster.
>
Not sure what you mean here or how it works.
>
> To adjust for covariates, I ran a regression with the 
> ExtractedClusterValues as the DV and Group, Sex, Age, and ICV as 
> predictors. Looking at the output, there was no significant effect of 
> group (p = .769; whereas in FreeSurfer the cluster-wise p < .001).
>
What were you using to do this test? You really need to have exactly the 
same design matrix and contrast matrix.
>
> Also when I plotted the predicted values adjusting for covariates, the 
> means between the groups were very similar.
>
>
> Why am I getting a p = .769 when I adjust for covariates, but 
> FreeSurfer has a cluster-wise p < .001? Or is there a way to calculate 
> adjusted values in FreeSurfer?
>
>
> Best,
>
>
> Jessica
>
>
>
> ___
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[Freesurfer] Group Analysis Covariates

[Hua, Jessica]

External Email - Use Caution

Dear Freesurfer Experts:


I analyzed my data following the guidelines on the FSL Tutorial/Group Analysis 
page . I am trying to plot the adjusted values (covariates: age, sex, and ICV) 
for the significant clusters for each of my participants.


I set up the contrast to test group differences. So testing whether there is a 
difference between groups regressing out the effects of sex, age, and ICV. 
Contrasts created were  [1 -1 0 0 0 0 0 0] and [-1 1 0 0 0 0 0 0].


I then extracted values from this file (cache.th20.abs.sig.y.ocn.dat; i.e., the 
average value of each subject in each cluster) into my dataset. I believe these 
are the unadjusted values, correct? I calculated total volume and total surface 
area by multiplying these values by the total number of vertices in each 
cluster. To adjust for covariates, I ran a regression with the 
ExtractedClusterValues as the DV and Group, Sex, Age, and ICV as predictors. 
Looking at the output, there was no significant effect of group (p = .769; 
whereas in FreeSurfer the cluster-wise p < .001). Also when I plotted the 
predicted values adjusting for covariates, the means between the groups were 
very similar.


Why am I getting a p = .769 when I adjust for covariates, but FreeSurfer has a 
cluster-wise p < .001? Or is there a way to calculate adjusted values in 
FreeSurfer?


Best,


Jessica
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Re: [Freesurfer] Group Analysis Contrast (Follow-up)

[Douglas Greve]

You need to put in age, weight, AND age*weight. If you have two classes 
and use DODS, then the contrast would be


0 0 0 0 0 0 0.5 0.5



On 4/13/18 8:02 PM, David S Lee wrote:

Hi Douglas,

Thank you for your reply.

To follow up, I am setting up GLM analysis with 1 categorical variable 
and 1 continuous variable (age X weight). Myfsgd looks like this:


/GroupDescriptorFile 1/
/Title Cortical Thickness Interaction between Age and Weight/
/Class class1 plus blue/
/Class class2 circle green/
/Variable           Demean Age X Demean Weight/
/Input001Class1500/
/Input002Class2433/
/.../

I want to test for an interaction between age and weight while 
controlling forgroup. Instead ofputting-inage and weight separately, I 
multiply them to test for interaction. Can you tell me if following 
contrast vector will correctly test for this?


/0 0 0.5 0.5/
/
/
Thank you for your time,
/
/
--
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115 


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[Freesurfer] Group Analysis Contrast (Follow-up)

[David S Lee]

Hi Douglas,

Thank you for your reply.

To follow up, I am setting up GLM analysis with 1 categorical variable and
1 continuous variable (age X weight). My fsgd looks like this:

*GroupDescriptorFile 1*
*Title Cortical Thickness Interaction between Age and Weight*
*Class class1 plus blue*
*Class class2 circle green*
*Variable   Demean Age X Demean Weight*
*Input 001 Class1 500*
*Input 002 Class2 433*
*...*

I want to test for an interaction between age and weight while controlling
for group. Instead of putting-in age and weight separately, I multiply them
to test for interaction. Can you tell me if following contrast vector will
correctly test for this?

*0 0 0.5 0.5*

Thank you for your time,

--
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] Group Analysis Design Matrix

[Douglas N. Greve]

If you want to test for an interaction between Age and Weight, you need 
to create a new covariate which is Age*Weight, then test the sig of this 
covariate. I would demean Age and Weight for both the inidvidual 
covaraite and before computing the product.


On 04/12/2018 12:35 PM, David S Lee wrote:
> Hi FreeSurfer Experts,
>
> I have two groups (Male and Female) and two covariates (Age and 
> Weight). I want to test change of cortical thickness with age and 
> weight, after removing effects of Group. In other words, is there an 
> interaction between age and weight, regressing out the effects of groups.
>
> How can I set up my Design Matrix to test this?
>
> Thank you,
>
> -- 
> David S. Lee
> Associate Research Specialist
> Center for Healthy Minds
> University of Wisconsin - Madison
> (608) 890-1115 
>
>
> ___
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[Freesurfer] Group Analysis Design Matrix

[David S Lee]

Hi FreeSurfer Experts,

I have two groups (Male and Female) and two covariates (Age and Weight). I
want to test change of cortical thickness with age and weight, after
removing effects of Group. In other words, is there an interaction between
age and weight, regressing out the effects of groups.

How can I set up my Design Matrix to test this?

Thank you,

-- 
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Re: [Freesurfer] group analysis on thickness/mask

[Douglas N Greve]

Pass it with --mask, not --label


On 09/11/2017 09:42 PM, Xianwei Che wrote:
> Dear Doug,
>
> After some trial and error I am still not able to run group analysis 
> in ROI manner.
>
> Here is my understanding: I need to define a label (mri_binarize ?) in 
> which my ROIs should be labeled as 1 with other regions being 0. Then 
> I can take this label to glm with --lable and then run correction. If 
> this is a right way can you tell me a little bit more of how to do 
> this. I am working on cortical thickness data.
>
> Thanks huge
>
>
>
> /-/
> Mr Xianwei Che
> PhD Candidate
> Monash Alfred Psychiatry Research Centre (MAPrc)
> Central Clinical School & the Alfred
> Monash University
> Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>
> On 12 September 2017 at 08:42, Xianwei Che  > wrote:
>
> Dear Doug,
>
> Thank you for the answer. I will try it out.
>
> Regards
>
> /-/
> Mr Xianwei Che
> PhD Candidate
> Monash Alfred Psychiatry Research Centre (MAPrc)
> Central Clinical School & the Alfred
> Monash University
> Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>
> On 12 September 2017 at 01:44, Douglas N Greve
> > wrote:
>
>
>
> On 09/10/2017 04:02 AM, Xianwei Che wrote:
> > Dear experts,
> >
> > I am going to run a group analysis on thickness but limit
> the results
> > to certain regions, say prefrontal cortex. l did find this
> thread but
> > failed to make it work on my data
> >
> 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html
> 
> ).
> > I know I could extract the signal of the ROI but also
> interested in
> > this way.
> >
> > Here are my questions:
> > 1. mri_binarize should be working on the average data or the
> single
> > data in each participant. If it should be on individual
> data, what the
> > loop should be (if I have a text file SUBJECTS listing the
> participants).
> Actually, I don't know what [subjects] is supposed to mean.
> You should
> include the index for the ROIs you want in the analysis
> > 2. How the --match is used. I --helped the mri_binarize but did not
> > get it. Is it for specifying the ROI by number, say the
> number of PFC?
> There is no PFC ROI. You will have to piece it together from
> other ROIs.
> You can get the full list from
> $FREESURFER_HOME/FreeSurferColorLUT.txt.
> Look in the section for aparc+aseg.mgz
> > 3. If I could finish the mask creation and merge to label; do I have
> > to undergo the data concatenating stage (i.e. preproc,
> surf2surf) or
> > directly move to glm. I saw another thread skipping these
> stages but
> > it's on volume data
> >
> 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html
> 
> ).
> Yu can move directly to the GLM
> >
> > Thank you so much!
> >
> >
> > /-/
> > Mr Xianwei Che
> > PhD Candidate
> > Monash Alfred Psychiatry Research Centre (MAPrc)
> > Central Clinical School & the Alfred
> > Monash University
> > Level 4, 607 St Kilda Road, Melbourne 3004, Australia
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> 
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
>
> ___
> Freesurfer mailing list
> 

Re: [Freesurfer] group analysis on thickness/mask

[Xianwei Che]

Dear Doug,

After some trial and error I am still not able to run group analysis in ROI
manner.

Here is my understanding: I need to define a label (mri_binarize ?) in
which my ROIs should be labeled as 1 with other regions being 0. Then I can
take this label to glm with --lable and then run correction. If this is a
right way can you tell me a little bit more of how to do this. I am working
on cortical thickness data.

Thanks huge



*-*
Mr Xianwei Che
PhD Candidate
Monash Alfred Psychiatry Research Centre (MAPrc)
Central Clinical School & the Alfred
Monash University
Level 4, 607 St Kilda Road, Melbourne 3004, Australia

On 12 September 2017 at 08:42, Xianwei Che  wrote:

> Dear Doug,
>
> Thank you for the answer. I will try it out.
>
> Regards
>
> *-*
> Mr Xianwei Che
> PhD Candidate
> Monash Alfred Psychiatry Research Centre (MAPrc)
> Central Clinical School & the Alfred
> Monash University
> Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>
> On 12 September 2017 at 01:44, Douglas N Greve 
> wrote:
>
>>
>>
>> On 09/10/2017 04:02 AM, Xianwei Che wrote:
>> > Dear experts,
>> >
>> > I am going to run a group analysis on thickness but limit the results
>> > to certain regions, say prefrontal  cortex. l did find this thread but
>> > failed to make it work on my data
>> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
>> /msg48693.html).
>> > I know I could extract the signal of the ROI but also interested in
>> > this way.
>> >
>> > Here are my questions:
>> > 1. mri_binarize should be working on the average data or the single
>> > data in each participant. If it should be on individual data, what the
>> > loop should be (if I have a text file SUBJECTS listing the
>> participants).
>> Actually, I don't know what [subjects] is supposed to mean. You should
>> include the index for the ROIs you want in the analysis
>> > 2. How the --match is used. I --helped the mri_binarize but did not
>> > get it. Is it for specifying the ROI by number, say the number of PFC?
>> There is no PFC ROI. You will have to piece it together from other ROIs.
>> You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt.
>> Look in the section for aparc+aseg.mgz
>> > 3. If I could finish the mask creation and merge to label; do I have
>> > to undergo the data concatenating stage (i.e. preproc, surf2surf) or
>> > directly move to glm. I saw another thread skipping these stages but
>> > it's on volume data
>> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
>> /msg32190.html).
>> Yu can move directly to the GLM
>> >
>> > Thank you so much!
>> >
>> >
>> > /-/
>> > Mr Xianwei Che
>> > PhD Candidate
>> > Monash Alfred Psychiatry Research Centre (MAPrc)
>> > Central Clinical School & the Alfred
>> > Monash University
>> > Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . 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.
>>
>>
>
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Re: [Freesurfer] group analysis on thickness/mask

[Xianwei Che]

Dear Doug,

Thank you for the answer. I will try it out.

Regards

*-*
Mr Xianwei Che
PhD Candidate
Monash Alfred Psychiatry Research Centre (MAPrc)
Central Clinical School & the Alfred
Monash University
Level 4, 607 St Kilda Road, Melbourne 3004, Australia

On 12 September 2017 at 01:44, Douglas N Greve 
wrote:

>
>
> On 09/10/2017 04:02 AM, Xianwei Che wrote:
> > Dear experts,
> >
> > I am going to run a group analysis on thickness but limit the results
> > to certain regions, say prefrontal  cortex. l did find this thread but
> > failed to make it work on my data
> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> edu/msg48693.html).
> > I know I could extract the signal of the ROI but also interested in
> > this way.
> >
> > Here are my questions:
> > 1. mri_binarize should be working on the average data or the single
> > data in each participant. If it should be on individual data, what the
> > loop should be (if I have a text file SUBJECTS listing the participants).
> Actually, I don't know what [subjects] is supposed to mean. You should
> include the index for the ROIs you want in the analysis
> > 2. How the --match is used. I --helped the mri_binarize but did not
> > get it. Is it for specifying the ROI by number, say the number of PFC?
> There is no PFC ROI. You will have to piece it together from other ROIs.
> You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt.
> Look in the section for aparc+aseg.mgz
> > 3. If I could finish the mask creation and merge to label; do I have
> > to undergo the data concatenating stage (i.e. preproc, surf2surf) or
> > directly move to glm. I saw another thread skipping these stages but
> > it's on volume data
> > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
> edu/msg32190.html).
> Yu can move directly to the GLM
> >
> > Thank you so much!
> >
> >
> > /-/
> > Mr Xianwei Che
> > PhD Candidate
> > Monash Alfred Psychiatry Research Centre (MAPrc)
> > Central Clinical School & the Alfred
> > Monash University
> > Level 4, 607 St Kilda Road, Melbourne 3004, Australia
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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 Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . 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.
>
>
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Re: [Freesurfer] group analysis on thickness/mask

[Douglas N Greve]

On 09/10/2017 04:02 AM, Xianwei Che wrote:
> Dear experts,
>
> I am going to run a group analysis on thickness but limit the results 
> to certain regions, say prefrontal  cortex. l did find this thread but 
> failed to make it work on my data 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html). 
> I know I could extract the signal of the ROI but also interested in 
> this way.
>
> Here are my questions:
> 1. mri_binarize should be working on the average data or the single 
> data in each participant. If it should be on individual data, what the 
> loop should be (if I have a text file SUBJECTS listing the participants).
Actually, I don't know what [subjects] is supposed to mean. You should 
include the index for the ROIs you want in the analysis
> 2. How the --match is used. I --helped the mri_binarize but did not 
> get it. Is it for specifying the ROI by number, say the number of PFC?
There is no PFC ROI. You will have to piece it together from other ROIs. 
You can get the full list from $FREESURFER_HOME/FreeSurferColorLUT.txt. 
Look in the section for aparc+aseg.mgz
> 3. If I could finish the mask creation and merge to label; do I have 
> to undergo the data concatenating stage (i.e. preproc, surf2surf) or 
> directly move to glm. I saw another thread skipping these stages but 
> it's on volume data 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html).
Yu can move directly to the GLM
>
> Thank you so much!
>
>
> /-/
> Mr Xianwei Che
> PhD Candidate
> Monash Alfred Psychiatry Research Centre (MAPrc)
> Central Clinical School & the Alfred
> Monash University
> Level 4, 607 St Kilda Road, Melbourne 3004, Australia
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.

[Freesurfer] group analysis on thickness/mask

[Xianwei Che]

Dear experts,

I am going to run a group analysis on thickness but limit the results to
certain regions, say prefrontal  cortex. l did find this thread but failed
to make it work on my data (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg48693.html).
I know I could extract the signal of the ROI but also interested in this
way.

Here are my questions:
1. mri_binarize should be working on the average data or the single data in
each participant. If it should be on individual data, what the loop should
be (if I have a text file SUBJECTS listing the participants).
2. How the --match is used. I --helped the mri_binarize but did not get it.
Is it for specifying the ROI by number, say the number of PFC?
3. If I could finish the mask creation and merge to label; do I have to
undergo the data concatenating stage (i.e. preproc, surf2surf) or directly
move to glm. I saw another thread skipping these stages but it's on volume
data (
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32190.html).

Thank you so much!


*-*
Mr Xianwei Che
PhD Candidate
Monash Alfred Psychiatry Research Centre (MAPrc)
Central Clinical School & the Alfred
Monash University
Level 4, 607 St Kilda Road, Melbourne 3004, Australia
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Re: [Freesurfer] group analysis of large data sets

[Douglas N Greve]

version 6 should be able to go up to 20,000


On 03/28/2017 11:45 AM, Wang, Xin wrote:
> Thank you, Dr. Greve.
> when I ran >2000 subjects in Version 5.3, I received this error message 
> "##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum 
> allowed 2000##"
> In your previous post about mri_glmfit, 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033151.html,
>  I found
> #define FSGDF_NCLASSES_MAX  128   
> #define FSGDF_NVARS_MAX 128   
> #define FSGDF_NINPUTS_MAX  2000   
> Are these the maximum? The mri_glmfit is written in C. Could you send me a 
> version of mri_glmfit code without limits?
> Thank you very much.
>
> Xin
>
> -Original Message-
> From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Monday, March 27, 2017 1:47 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] group analysis of large data sets
>
> I don't think there is a maximum size. You would do the big analysis the same 
> way as the small.
>
>
> On 03/26/2017 07:54 PM, Wang, Xin wrote:
>> Hello, FreeSurfer Group,
>>
>> What is the maximal matrix size for glm_fit process?
>>
>> How to use FreeSurfer for group analyses of more than 2000 subjects,
>> 128 variables, and 128 Classes?
>>
>> Thank you.
>>
>> Xin
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] group analysis of large data sets

[Wang, Xin]

Thank you, Dr. Greve.
when I ran >2000 subjects in Version 5.3, I received this error message 
"##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum 
allowed 2000##"
In your previous post about mri_glmfit, 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033151.html,
 I found
#define FSGDF_NCLASSES_MAX  128 
#define FSGDF_NVARS_MAX 128 
#define FSGDF_NINPUTS_MAX  2000 
Are these the maximum? The mri_glmfit is written in C. Could you send me a 
version of mri_glmfit code without limits?
Thank you very much.

Xin

-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] 
Sent: Monday, March 27, 2017 1:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] group analysis of large data sets

I don't think there is a maximum size. You would do the big analysis the same 
way as the small.


On 03/26/2017 07:54 PM, Wang, Xin wrote:
>
> Hello, FreeSurfer Group,
>
> What is the maximal matrix size for glm_fit process?
>
> How to use FreeSurfer for group analyses of more than 2000 subjects, 
> 128 variables, and 128 Classes?
>
> Thank you.
>
> Xin
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/



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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] group analysis of large data sets

[Douglas N Greve]

I don't think there is a maximum size. You would do the big analysis the 
same way as the small.


On 03/26/2017 07:54 PM, Wang, Xin wrote:
>
> Hello, FreeSurfer Group,
>
> What is the maximal matrix size for glm_fit process?
>
> How to use FreeSurfer for group analyses of more than 2000 subjects, 
> 128 variables, and 128 Classes?
>
> Thank you.
>
> Xin
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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dispose of the e-mail.

[Freesurfer] group analysis of large data sets

[Wang, Xin]

Hello, FreeSurfer Group,

What is the maximal matrix size for glm_fit process?
How to use FreeSurfer for group analyses of more than 2000 subjects, 128 
variables, and 128 Classes?

Thank you.

Xin
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Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

[Xiuyi Wang]

Hello Bruce,

Thank you so much.

I will try later.

Xiuyi

On 2 March 2017 at 17:11, Douglas N Greve  wrote:

> Click the button that says to show the annotation in outline (since you
> could not load it in outline mode
>
>
> On 03/02/2017 11:50 AM, Xiuyi Wang wrote:
> > Hi Bruce,
> >
> > Sorry for the misunderstanding.
> >
> > After showing the message "Did not find any volume geometry
> > information in the surface", the FreeView shows this image. It is not
> > the same as the tutorial website.
> >
> >
> > ​
> > Is there anything I can do to view the data?
> >
> > Thank you.
> >
> > Xiuyi
> >
> > On 2 March 2017 at 16:31, Douglas N Greve  > > wrote:
> >
> > when you say it stops, you mean it crashes and returns control to the
> > command line? Or that the GUI stays up but is unresponsive?
> >
> >
> > On 03/02/2017 11:29 AM, Xiuyi Wang wrote:
> > > Hello Bruce,
> > >
> > > The program stops after displaying this message.
> > >
> > > So I guess your solution is to use FreeSurfer 6 and I am not able
> to
> > > view the data using FreeSurfer 5.3.
> > >
> > > Thanks.
> > >
> > > Xiuyi
> > >
> > > On 2 March 2017 at 16:26, Douglas N Greve
> > 
> > >  edu>>> wrote:
> > >
> > > That is not an error, the program should have run normally
> > after that.
> > > This has been fixed in v6.
> > >
> > >
> > > On 03/02/2017 11:23 AM, Xiuyi Wang wrote:
> > > > Hello Bruce,
> > > >
> > > > Thank you for your reply.
> > > >
> > > > I have tried to delete “:annot_outline=1: before andthe
> > command
> > > lines are:
> > > >
> > > > freeview -f
> > > >
> > >
> >  $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:
> overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.
> mgh:overlay_threshold=4,5
> > > > -viewport 3d
> > > >
> > > > But I received another error message:
> > > >
> > > > Did not find any volume geometry information in the surface.
> > > >
> > > > So I still can not view the data.
> > > >
> > > > Thanks.
> > > >
> > > > Xiuyi
> > > >
> > > > On 2 March 2017 at 16:01, Douglas N Greve
> > >  > 
> >  >>
> > > > 
> > >  >  > > >
> > > > You can use that command, just remove annot_outline=1:
> > > >
> > > >
> > > > On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
> > > > > Hi,
> > > > >
> > > > > I am learning Group Analysis using FreeSurfer 5.3 on
> > Linux
> > > system.
> > > > >
> > > > > I followed the detailed instruction on the tutorial
> > website.
> > > > >
> > > > >
> > > >
> > >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> > 
> > >
> >   >  >>
> > > >
> > >
> >  > 
> > >
> >   >  >>>
> > > > >
> > > >
> > >
> >  > 
> > >
> >   >  >>
> > > >
> > >
> >  > 
> > >
> >   >  
> > > > >
> > > > > These are the commands that I typed:
> > > > >
> > > > > freeview
> > > > >
> > > >
> > >
> > 

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

[Douglas N Greve]

when you say it stops, you mean it crashes and returns control to the 
command line? Or that the GUI stays up but is unresponsive?


On 03/02/2017 11:29 AM, Xiuyi Wang wrote:
> Hello Bruce,
>
> The program stops after displaying this message.
>
> So I guess your solution is to use FreeSurfer 6 and I am not able to 
> view the data using FreeSurfer 5.3.
>
> Thanks.
>
> Xiuyi
>
> On 2 March 2017 at 16:26, Douglas N Greve  > wrote:
>
> That is not an error, the program should have run normally after that.
> This has been fixed in v6.
>
>
> On 03/02/2017 11:23 AM, Xiuyi Wang wrote:
> > Hello Bruce,
> >
> > Thank you for your reply.
> >
> > I have tried to delete “:annot_outline=1: before andthe command
> lines are:
> >
> > freeview -f
> >
> 
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> > -viewport 3d
> >
> > But I received another error message:
> >
> > Did not find any volume geometry information in the surface.
> >
> > So I still can not view the data.
> >
> > Thanks.
> >
> > Xiuyi
> >
> > On 2 March 2017 at 16:01, Douglas N Greve
> 
> >  >> wrote:
> >
> > You can use that command, just remove annot_outline=1:
> >
> >
> > On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
> > > Hi,
> > >
> > > I am learning Group Analysis using FreeSurfer 5.3 on Linux
> system.
> > >
> > > I followed the detailed instruction on the tutorial website.
> > >
> > >
> >
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> 
> >   
>   >
> > >
> >   
>   
> >   
>   >>
> > >
> > > These are the commands that I typed:
> > >
> > > freeview
> > >
> >   
>  
> -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:
> > >
> overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg
> 
> > 
> > > h:overlay_thres
> > > hold=4,5 -viewport 3d
> > >
> > > But I got an error message "Unrecognized sub-option flag
> > > ‘annot_outline’ " when running this command to visualize
> uncorrected
> > > significance map with freeview.
> > >
> > > Douglas Greve told me it's because the outline only works
> on 6.0.
> > >
> > > I am wondering what commands should I use to visualize the
> > uncorrected
> > > significance map with freeview 5.3.
> > >
> > > Thank you for your help.
> > >
> > >
> > > On 10 February 2017 at 17:47, Douglas Greve
> > >  
> >  >
> >  
> >   > >
> > > The outline only works on 6.0
> > >
> > >
> > > On 2/10/17 11:57 AM, Xiuyi Wang wrote:
> > >>
> > >> Hi,
> > >>
> > >>
> > >> I am learning GroupAnalysis using FreeSurfer 5.3 on
> > Linux system.
> > >>
> > >>
> > >> I followed the detailed instruction on the tutorial
> > website.
> > >>
> > >>
> >
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> 
> >   
>   >
> > >>
> > 
>  
> >   
>   

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

[Xiuyi Wang]

Hello Bruce,

Thank you for your reply.

I have tried to delete “:annot_outline=1: before and the command lines are:

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o
verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
-viewport 3d



But I received another error message:
Did not find any volume geometry information in the surface.

So I still can not view the data.

Thanks.

Xiuyi

On 2 March 2017 at 16:01, Douglas N Greve  wrote:

> You can use that command, just remove annot_outline=1:
>
>
> On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
> > Hi,
> >
> > I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
> >
> > I followed the detailed instruction on the tutorial website.
> >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> > 
> >
> > These are the commands that I typed:
> >
> > freeview
> > -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.
> annot:annot_outline=1:
> > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg
> > h:overlay_thres
> > hold=4,5 -viewport 3d
> >
> > But I got an error message "Unrecognized sub-option flag
> > ‘annot_outline’ " when running this command to visualize uncorrected
> > significance map with freeview.
> >
> > Douglas Greve told me it's because the outline only works on 6.0.
> >
> > I am wondering what commands should I use to visualize the uncorrected
> > significance map with freeview 5.3.
> >
> > Thank you for your help.
> >
> >
> > On 10 February 2017 at 17:47, Douglas Greve
> > >
> wrote:
> >
> > The outline only works on 6.0
> >
> >
> > On 2/10/17 11:57 AM, Xiuyi Wang wrote:
> >>
> >> Hi,
> >>
> >>
> >> I am learning GroupAnalysis using FreeSurfer 5.3 on Linux
> system.
> >>
> >>
> >> I followed the detailed instruction on the tutorial website.
> >>
> >> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/
> GroupAnalysis
> >>  GroupAnalysis>
> >>
> >>
> >> But I got an error message when running this command to
> >> visualize uncorrected significance map with freeview.
> >>
> >>
> >> This is the command I typed:
> >>
> >> freeview -f
> >> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:
> annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-
> thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> >> -viewport 3d
> >>
> >> I received this error message:
> >>
> >> Unrecognized sub-option flag ‘annot_outline’
> >>
> >>
> >> I browsed the internet and found that “That option is only
> >> available in the development version of freeview. You can try
> >> removing :annot_ouline=1 from the command-line and turn it on
> >> manually from the GUI.”
> >>
> >>
> >> So I deleted “:annot_outline=1” and the command line is :
> >>
> >> freeview -f
> >> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:
> overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.
> mgh:overlay_threshold=4,5
> >> -viewport 3d
> >>
> >> But I received another error message:
> >>
> >> Did not find any volume geometry information in the surface.
> >>
> >>
> >> I found some researchers also have encountered this problem,
> >> but it has not been solved.
> >>
> >>
> >> Could you please tell me the solution of the problem?
> >>
> >> Thank you for your suggestion.
> >>
> >>
> >> Best.
> >>
> >> Xiuyi Wang
> >>
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> 
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >> 
> > ___ Freesurfer
> > mailing list Freesurfer@nmr.mgh.harvard.edu
> > 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > 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 Partners Compliance HelpLine at
> > http://www.partners.org/complianceline
> >  . If the e-mail was
> > sent to you in error but does not contain patient information,
> > please contact the sender and properly 

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

[Xiuyi Wang]

Hello Bruce,

The program stops after displaying this message.

So I guess your solution is to use FreeSurfer 6 and I am not able to view
the data using FreeSurfer 5.3.

Thanks.

Xiuyi

On 2 March 2017 at 16:26, Douglas N Greve  wrote:

> That is not an error, the program should have run normally after that.
> This has been fixed in v6.
>
>
> On 03/02/2017 11:23 AM, Xiuyi Wang wrote:
> > Hello Bruce,
> >
> > Thank you for your reply.
> >
> > I have tried to delete “:annot_outline=1: before andthe command lines
> are:
> >
> > freeview -f
> > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:
> overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.
> mgh:overlay_threshold=4,5
> > -viewport 3d
> >
> > But I received another error message:
> >
> > Did not find any volume geometry information in the surface.
> >
> > So I still can not view the data.
> >
> > Thanks.
> >
> > Xiuyi
> >
> > On 2 March 2017 at 16:01, Douglas N Greve  > > wrote:
> >
> > You can use that command, just remove annot_outline=1:
> >
> >
> > On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
> > > Hi,
> > >
> > > I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
> > >
> > > I followed the detailed instruction on the tutorial website.
> > >
> > >
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> > 
> > >
> >  >  >>
> > >
> > > These are the commands that I typed:
> > >
> > > freeview
> > >
> > -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.
> annot:annot_outline=1:
> > > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg
> > 
> > > h:overlay_thres
> > > hold=4,5 -viewport 3d
> > >
> > > But I got an error message "Unrecognized sub-option flag
> > > ‘annot_outline’ " when running this command to visualize
> uncorrected
> > > significance map with freeview.
> > >
> > > Douglas Greve told me it's because the outline only works on 6.0.
> > >
> > > I am wondering what commands should I use to visualize the
> > uncorrected
> > > significance map with freeview 5.3.
> > >
> > > Thank you for your help.
> > >
> > >
> > > On 10 February 2017 at 17:47, Douglas Greve
> > >  > 
> >  > >> wrote:
> > >
> > > The outline only works on 6.0
> > >
> > >
> > > On 2/10/17 11:57 AM, Xiuyi Wang wrote:
> > >>
> > >> Hi,
> > >>
> > >>
> > >> I am learning GroupAnalysis using FreeSurfer 5.3 on
> > Linux system.
> > >>
> > >>
> > >> I followed the detailed instruction on the tutorial
> > website.
> > >>
> > >>
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> > 
> > >>
> >   >  >>
> > >>
> > >>
> > >> But I got an error message when running this command to
> > >> visualize uncorrected significance map with freeview.
> > >>
> > >>
> > >> This is the command I typed:
> > >>
> > >> freeview -f
> > >>
> >  $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:
> annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-
> thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> > >> -viewport 3d
> > >>
> > >> I received this error message:
> > >>
> > >> Unrecognized sub-option flag ‘annot_outline’
> > >>
> > >>
> > >> I browsed the internet and found that “That option is only
> > >> available in the development version of freeview. You
> > can try
> > >> removing :annot_ouline=1 from the command-line and turn
> > it on
> > >> manually from the GUI.”
> > >>
> > >>
> > >> So I deleted “:annot_outline=1” and the command line is :
> > >>
> > >> freeview -f
> > >>
> >  $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:
> overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.
> mgh:overlay_threshold=4,5
> > >> -viewport 3d
> > >>
> > >> But I received another error message:
> > >>
> > >> Did not find any volume geometry information in the
> > surface.
> > >>
> 

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

[Douglas N Greve]

That is not an error, the program should have run normally after that. 
This has been fixed in v6.


On 03/02/2017 11:23 AM, Xiuyi Wang wrote:
> Hello Bruce,
>
> Thank you for your reply.
>
> I have tried to delete “:annot_outline=1: before andthe command lines are:
>
> freeview -f 
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
>  
> -viewport 3d
>
> But I received another error message:
>
> Did not find any volume geometry information in the surface.
>
> So I still can not view the data.
>
> Thanks.
>
> Xiuyi
>
> On 2 March 2017 at 16:01, Douglas N Greve  > wrote:
>
> You can use that command, just remove annot_outline=1:
>
>
> On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
> > Hi,
> >
> > I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
> >
> > I followed the detailed instruction on the tutorial website.
> >
> >
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> 
> >
>  >
> >
> > These are the commands that I typed:
> >
> > freeview
> >
> 
> -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:
> > overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg
> 
> > h:overlay_thres
> > hold=4,5 -viewport 3d
> >
> > But I got an error message "Unrecognized sub-option flag
> > ‘annot_outline’ " when running this command to visualize uncorrected
> > significance map with freeview.
> >
> > Douglas Greve told me it's because the outline only works on 6.0.
> >
> > I am wondering what commands should I use to visualize the
> uncorrected
> > significance map with freeview 5.3.
> >
> > Thank you for your help.
> >
> >
> > On 10 February 2017 at 17:47, Douglas Greve
> >  
>  >> wrote:
> >
> > The outline only works on 6.0
> >
> >
> > On 2/10/17 11:57 AM, Xiuyi Wang wrote:
> >>
> >> Hi,
> >>
> >>
> >> I am learning GroupAnalysis using FreeSurfer 5.3 on
> Linux system.
> >>
> >>
> >> I followed the detailed instruction on the tutorial
> website.
> >>
> >>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> 
> >>   
>   >
> >>
> >>
> >> But I got an error message when running this command to
> >> visualize uncorrected significance map with freeview.
> >>
> >>
> >> This is the command I typed:
> >>
> >> freeview -f
> >>   
>  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> >> -viewport 3d
> >>
> >> I received this error message:
> >>
> >> Unrecognized sub-option flag ‘annot_outline’
> >>
> >>
> >> I browsed the internet and found that “That option is only
> >> available in the development version of freeview. You
> can try
> >> removing :annot_ouline=1 from the command-line and turn
> it on
> >> manually from the GUI.”
> >>
> >>
> >> So I deleted “:annot_outline=1” and the command line is :
> >>
> >> freeview -f
> >>   
>  
> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
> >> -viewport 3d
> >>
> >> But I received another error message:
> >>
> >> Did not find any volume geometry information in the
> surface.
> >>
> >>
> >> I found some researchers also have encountered this
> problem,
> >> but it has not been solved.
> >>
> >>
> >> Could you please tell me the solution of the problem?
> >>
> >> Thank you for your suggestion.
> >>
> >>
> >> Best.
> >>
> >> Xiuyi Wang
> >>
> >>
> >>
> >>
> >> ___
> >> Freesurfer mailing list
> >> 

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

[Douglas N Greve]

You can use that command, just remove annot_outline=1:


On 03/02/2017 07:18 AM, Xiuyi Wang wrote:
> Hi,
>
> I am learning Group Analysis using FreeSurfer 5.3 on Linux system.
>
> I followed the detailed instruction on the tutorial website.
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 
> 
>
> These are the commands that I typed:
>
> freeview 
> -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:
> overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mg 
> h:overlay_thres
> hold=4,5 -viewport 3d
>
> But I got an error message "Unrecognized sub-option flag 
> ‘annot_outline’ " when running this command to visualize uncorrected 
> significance map with freeview.
>
> Douglas Greve told me it's because the outline only works on 6.0.
>
> I am wondering what commands should I use to visualize the uncorrected 
> significance map with freeview 5.3.
>
> Thank you for your help.
>
>
> On 10 February 2017 at 17:47, Douglas Greve
> > wrote:
>
> The outline only works on 6.0
>
>
> On 2/10/17 11:57 AM, Xiuyi Wang wrote:
>>
>> Hi,
>>
>>
>> I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system.
>>
>>
>> I followed the detailed instruction on the tutorial website.
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>> 
>>
>>
>> But I got an error message when running this command to
>> visualize uncorrected significance map with freeview.
>>
>>
>> This is the command I typed:
>>
>> freeview -f
>> 
>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
>> -viewport 3d
>>
>> I received this error message:
>>
>> Unrecognized sub-option flag ‘annot_outline’
>>
>>
>> I browsed the internet and found that “That option is only
>> available in the development version of freeview. You can try
>> removing :annot_ouline=1 from the command-line and turn it on
>> manually from the GUI.”
>>
>>
>> So I deleted “:annot_outline=1” and the command line is :
>>
>> freeview -f
>> 
>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
>> -viewport 3d
>>
>> But I received another error message:
>>
>> Did not find any volume geometry information in the surface.
>>
>>
>> I found some researchers also have encountered this problem,
>> but it has not been solved.
>>
>>
>> Could you please tell me the solution of the problem?
>>
>> Thank you for your suggestion.
>>
>>
>> Best.
>>
>> Xiuyi Wang
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
> ___ Freesurfer
> mailing list Freesurfer@nmr.mgh.harvard.edu
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 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 Partners Compliance HelpLine at
> http://www.partners.org/complianceline
>  . 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. 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

[Xiuyi Wang]

Hi,

I am learning Group Analysis using FreeSurfer 5.3 on Linux system.

I followed the detailed instruction on the tutorial website.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

These are the commands that I typed:

freeview -f$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot
:annot_outline=1:
overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_thres
hold=4,5 -viewport 3d

But I got an error message "Unrecognized sub-option flag ‘annot_outline’ " when
running this command to visualize uncorrected significance map with
freeview.

Douglas Greve told me it's because the outline only works on 6.0.

I am wondering what commands should I use to visualize the uncorrected
significance map with freeview 5.3.

Thank you for your help.


> On 10 February 2017 at 17:47, Douglas Greve 
> wrote:
>
>> The outline only works on 6.0
>>
>> On 2/10/17 11:57 AM, Xiuyi Wang wrote:
>>
>> Hi,
>>
>>
>> I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system.
>>
>>
>> I followed the detailed instruction on the tutorial website.
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>
>>
>> But I got an error message when running this command to visualize
>> uncorrected significance map with freeview.
>>
>>
>> This is the command I typed:
>>
>> freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:a
>> nnot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness
>> -age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d
>>
>>
>>
>> I received this error message:
>>
>> Unrecognized sub-option flag ‘annot_outline’
>>
>>
>> I browsed the internet and found that “That option is only available in
>> the development version of freeview. You can try removing :annot_ouline=1
>> from the command-line and turn it on manually from the GUI.”
>>
>>
>> So I deleted “:annot_outline=1” and the command line is :
>>
>> freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o
>> verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
>> -viewport 3d
>>
>>
>>
>> But I received another error message:
>>
>> Did not find any volume geometry information in the surface.
>>
>>
>> I found some researchers also have encountered this problem, but it has
>> not been solved.
>>
>>
>> Could you please tell me the solution of the problem?
>>
>> Thank you for your suggestion.
>>
>>
>> Best.
>>
>> Xiuyi Wang
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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 Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . 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.
>>
>>
>
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Re: [Freesurfer] Fwd: FreeSurfer group analysis visualize data

[Douglas Greve]

The outline only works on 6.0


On 2/10/17 11:57 AM, Xiuyi Wang wrote:


Hi,


I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system.


I followed the detailed instruction on the tutorial website.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis 




But I got an error message when running this command to visualize 
uncorrected significance map with freeview.



This is the command I typed:

freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 
-viewport 3d


I received this error message:

Unrecognized sub-option flag ‘annot_outline’


I browsed the internet and found that “That option is only available 
in the development version of freeview. You can try removing 
:annot_ouline=1 from the command-line and turn it on manually from the 
GUI.”



So I deleted “:annot_outline=1” and the command line is :

freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 
-viewport 3d


But I received another error message:

Did not find any volume geometry information in the surface.


I found some researchers also have encountered this problem, but it 
has not been solved.



Could you please tell me the solution of the problem?

Thank you for your suggestion.


Best.

Xiuyi Wang




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[Freesurfer] Fwd: FreeSurfer group analysis visualize data

[Xiuyi Wang]

Hi,


I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system.


I followed the detailed instruction on the tutorial website.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis


But I got an error message when running this command to visualize
uncorrected significance map with freeview.


This is the command I typed:

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:a
nnot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness
-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d



I received this error message:

Unrecognized sub-option flag ‘annot_outline’


I browsed the internet and found that “That option is only available in the
development version of freeview. You can try removing :annot_ouline=1 from
the command-line and turn it on manually from the GUI.”


So I deleted “:annot_outline=1” and the command line is :

freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o
verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5
-viewport 3d



But I received another error message:

Did not find any volume geometry information in the surface.


I found some researchers also have encountered this problem, but it has not
been solved.


Could you please tell me the solution of the problem?

Thank you for your suggestion.


Best.

Xiuyi Wang
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Re: [Freesurfer] Group analysis Cortical Thickness

[Douglas Greve]

Check out the group analysis tutorial

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

On 10/26/16 7:11 AM, Dev vasu wrote:

Dear Freesurfer Group,

I would like to perform group analysis for 50 Subjects (25 healthy 
controls and 25 Subjects with BLVP  ) and examine the changes in 
cortical thickness between 2 groups, could you please kindly inform me 
some methods that i should adapt to perform the analysis.



Thanks
Vasudev


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[Freesurfer] Group analysis Cortical Thickness

[Dev vasu]

Dear Freesurfer Group,

I would like to perform group analysis for 50 Subjects (25 healthy controls
and 25 Subjects with BLVP  ) and examine the changes in cortical thickness
between 2 groups, could you please kindly inform me some methods that i
should adapt to perform the analysis.


Thanks
Vasudev
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[Freesurfer] Group analysis in repeated measures anova

[Greenberg, Jonathan]

Dear Freesurfer users
I am trying to examine differences between 3 groups in surface thickness and 
volume over three time periods (pre-intervention, post-intervention, and 
6-month followup). Previously, when only the first 2 time points were 
available, I followed the instructions for paired analysis detailed in 
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis. In the FSGD file, 
Group was the only Class. 
Now that I have 3 time points, I am trying to follow the instructions for 
repeated measures anova detailed in 
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. The FSGD file 
structure in this case is different, with each single participant having their 
own Class (i.e. in my case – 60 Classes for the 60 participants), and 2 
variables contrasting the time points

GroupDescriptorFile 1
Class Subject1
Class Subject2
Class Subject3
VariablesTP1-vs-TP2 TP1-vs-TP3
Input subject1-tp1  Subject1 1  1
Input subject1-tp2  Subject1-1  0 
Input subject1-tp3  Subject1 0 -1
Input subject2-tp1  Subject2 1  1
Input subject2-tp2  Subject2-1  0 
Input subject2-tp3  Subject2 0 -1 
Input subject3-tp1  Subject3 1  1
Input subject3-tp2  Subject3-1  0 
Input subject3-tp3  Subject3 0 -1
In this case – the design matrix is
(Sub1)  (Sub2)  (Sub3)  (V1)(v2)
1   0   0   1   1
1   0   0   -1  0
1   0   0   0   -1
0   1   0   1   1
0   1   0   -1  0
0   1   0   0   -1
0   0   1   1   1
0   0   1   -1  0
0   0   1   0   -1

My question is whether and how can I incorporate participants' group (a 
between-subject variable) into this FSGD file? Should 3 additional Classes 
simply be added, one for each group, thereby making the new FSGD file as follows

GroupDescriptorFile 1   
Class   Group1  
Class   Group2  
Class   Group3  
Class   Subject1
Class   Subject2
Class   Subject3
Variables   TP1-vs-TP2  TP1-vs-TP3
Input   subject1-tp1Subject1Group3  1   1
Input   subject1-tp2Subject1Group3  -1  0
Input   subject1-tp3Subject1Group3  0   -1
Input   subject2-tp1Subject2Group2  1   1
Input   subject2-tp2Subject2Group2  -1  0
Input   subject2-tp3Subject2Group2  0   -1
Input   subject3-tp1Subject3Group3  1   1
Input   subject3-tp2Subject3Group3  -1  0
Input   subject3-tp3Subject3Group3  0   -1
and the matrix design as follows?
(Group1)(Group2)(Group3)(Sub1)(Sub2) (Sub3) (V1)(v2)
0   0   1   1   0   0   1   1
0   0   1   1   0   0   -1  0
0   0   1   1   0   0   0   -1
0   1   0   0   1   0   1   1
0   1   0   0   1   0   -1  0
0   1   0   0   1   0   0   -1
0   0   1   0   0   1   1   1
0   0   1   0   0   1   -1  0
0   0   1   0   0   1   0   -1
Thank you
Jonathan 
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Re: [Freesurfer] group analysis

[Douglas Greve]

Both contrasts are right. You might want to change the value from 0.5 to 
1/6, but that won't affect the actual p-values (only the gamma values). 
The 2nd contrast is correct, but it maybe difficult to interpret if the 
first contrast has an effect. Technically, you should verify that there 
is no interaction between group and continuous covariates. If there is 
no effect, then re-run with DOSS (the non-interaction model).



On 10/12/16 1:01 PM, charles laidi wrote:

Dear Douglas and Trisanna,

Thank you very much for your explanations.

I just would like to be sure of what I am doing since there is no 
example on the wiki as complex as mine.


If I have the following classes :

Diagnosis : Patient or Control
Gender : Male or Female
Site : Site1 or Site2 or Site3

NregressorsDODS = Nclasses*(Nvariables+1) = 6*(0+1) = 2*2*3*(1+1) = 24
Regressor1: ones for PatientMaleSite1 subjects, 0 otherwise. Codes 
intercept for Group 1
Regressor2: ones for PatientMaleSite2 subjects, 0 otherwise. Codes 
intercept for Group 2
Regressor2: ones for PatientMaleSite3 subjects, 0 otherwise. Codes 
intercept for Group 3


Regressor12: ones for ControlFemaleSite3 subjects, 0 otherwise. Codes 
intercept for Group 12
Regressor13: age for PatientMaleSite1 subjects, 0 otherwise. Codes age 
slope for Group 1
Regressor14: age for PatientMaleSite2 subjects, 0 otherwise. Codes age 
slope for Group 2

...
Regressor24: age for ControlFemaleSite3 subjects, 0 otherwise. Codes 
age slope for Group 12


*I assume my FSGDF file should look like : *

GroupDescriptorFile 1
Title analysis
Class PatientMaleSite1
Class PatientMaleSite2
Class PatientMaleSite3
Class PatientFemaleSite1
Class PatientFemaleSite2
Class PatientFemaleSite3
Class ControlMaleSite1
Class ControlMaleSite2
Class ControlMaleSite3
Class ControlFemaleSite1
Class ControlFemaleSite2
Class ControlFemaleSite3
Variables Age
Input subject1 PatientMaleSite1 30
Input subject2 PatientFemaleSite2 45
Input subject3 PatientFemaleSite3 85
Input subject4 PatientFemaleSite4 75
...

As for the contrast analysis :

If my question is : *is there a difference between Patient and 
Controls age slope regressing out the effects of gender and site? *


_Contrast1 patient-control.slope.mtx_

0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 
-0.5 -0.5


with all regressor1 to regressor12 equal to *0*
with regressor13 to 18 equal to *0.5 *(regressor with Patient in it)
with regressor19 to 24 equal to *- 0.5* (regressor with Controls in it)

If my question is :*is there a difference between cortical thickness 
in patients and controls, regressing out the effects of age, gender 
and site ? *


_Contrast2 patient-controls.mtx_

0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 
0 0 0 0


with all regressor1 to regressor6 equal to *0.5
*with all regressor7 to regressor12 equal to -*0.5*
with all regressor13 to regressor24 equal to *0*

Thank you very much in advance for your help and sorry for taking your 
time.


Best,

Charles










2016-10-05 17:44 GMT+02:00 Douglas N Greve >:


This is a straightforward extension to the FSGD examples. You have 3
discrete factors (2 diagnosis, 2 gender, 6 centers), this yields
2*2*6=24 classes. With one covariate, you would have 24 covariate
regressors (one for each class) for a total of 48. You would then need
to create a contrast matrix that tests for an interaction between
diagnosis and age which is also a straight-forward extension to the
examples.

Having said that, I think that 48 regressors is a lot unless you have
about 500 subjects. It is also possible to have a less agressive model
and just have two regressors, one for each diagnosis. But you'd
have to
create the design matrix yourself as this is outside of the FSGD
specification.


On 10/05/2016 09:22 AM, charles laidi wrote:
> Dear FreeSurfers,
>
> I would like to study the interaction between age and cortical
> thickness in patients and controls.
> My hypothesis is that there is an interaction and that cortical
> thickness is decreasing faster with age in patients than in
controls.
> I have both Male and Female included in 6 different centers.
> I would like to consider also Gender and Site (6 centers) as
confounds.
>
> My understanding is that I should perform a surface based group
> analysis with freesurfer.
>
> I am not able to find an example for my problem in the documentation
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V

>
> Would anyone had some tips to build the Fsgd file and the
contrast file ?
>
> Thank you very much in advance.
>
> Best,
>
> Charles
>
>
>
> ___
> Freesurfer mailing list
> 

Re: [Freesurfer] group analysis

[charles laidi]

Dear Douglas and Trisanna,

Thank you very much for your explanations.

I just would like to be sure of what I am doing since there is no example
on the wiki as complex as mine.

If I have the following classes :

Diagnosis : Patient or Control
Gender : Male or Female
Site : Site1 or Site2 or Site3

NregressorsDODS = Nclasses*(Nvariables+1) = 6*(0+1) = 2*2*3*(1+1) = 24
Regressor1: ones for PatientMaleSite1 subjects, 0 otherwise. Codes
intercept for Group 1
Regressor2: ones for PatientMaleSite2 subjects, 0 otherwise. Codes
intercept for Group 2
Regressor2: ones for PatientMaleSite3 subjects, 0 otherwise. Codes
intercept for Group 3

Regressor12: ones for ControlFemaleSite3 subjects, 0 otherwise. Codes
intercept for Group 12
Regressor13: age for PatientMaleSite1 subjects, 0 otherwise. Codes age
slope for Group 1
Regressor14: age for PatientMaleSite2 subjects, 0 otherwise. Codes age
slope for Group 2
...
Regressor24: age for ControlFemaleSite3 subjects, 0 otherwise. Codes age
slope for Group 12

*I assume my FSGDF file should look like : *

GroupDescriptorFile 1
Title analysis
Class PatientMaleSite1
Class PatientMaleSite2
Class PatientMaleSite3
Class PatientFemaleSite1
Class PatientFemaleSite2
Class PatientFemaleSite3
Class ControlMaleSite1
Class ControlMaleSite2
Class ControlMaleSite3
Class ControlFemaleSite1
Class ControlFemaleSite2
Class ControlFemaleSite3
Variables Age
Input subject1 PatientMaleSite1 30
Input subject2 PatientFemaleSite2 45
Input subject3 PatientFemaleSite3 85
Input subject4 PatientFemaleSite4 75
...

As for the contrast analysis :

If my question is : *is there a difference between Patient and Controls age
slope regressing out the effects of gender and site? *

*Contrast1 patient-control.slope.mtx*

0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5
-0.5

with all regressor1 to regressor12 equal to *0*
with regressor13 to 18 equal to *0.5  *(regressor with Patient in it)
with regressor19 to 24 equal to *- 0.5* (regressor with Controls in it)

If my question is :* is there a difference between cortical thickness in
patients and controls, regressing out the effects of age, gender and site ?
*

*Contrast2 patient-controls.mtx*

0.5 0.5 0.5 0.5 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0
0

with all regressor1 to regressor6 equal to
*0.5*with all regressor7 to regressor12 equal to -*0.5*
with all regressor13 to regressor24 equal to *0*

Thank you very much in advance for your help and sorry for taking your
time.

Best,

Charles










2016-10-05 17:44 GMT+02:00 Douglas N Greve :

> This is a straightforward extension to the FSGD examples. You have 3
> discrete factors (2 diagnosis, 2 gender, 6 centers), this yields
> 2*2*6=24 classes. With one covariate, you would have 24 covariate
> regressors (one for each class) for a total of 48. You would then need
> to create a contrast matrix that tests for an interaction between
> diagnosis and age which is also a straight-forward extension to the
> examples.
>
> Having said that, I think that 48 regressors is a lot unless you have
> about 500 subjects. It is also possible to have a less agressive model
> and just have two regressors, one for each diagnosis. But you'd have to
> create the design matrix yourself as this is outside of the FSGD
> specification.
>
>
> On 10/05/2016 09:22 AM, charles laidi wrote:
> > Dear FreeSurfers,
> >
> > I would like to study the interaction between age and cortical
> > thickness in patients and controls.
> > My hypothesis is that there is an interaction and that cortical
> > thickness is decreasing faster with age in patients than in controls.
> > I have both Male and Female included in 6 different centers.
> > I would like to consider also Gender and Site (6 centers) as confounds.
> >
> > My understanding is that I should perform a surface based group
> > analysis with freesurfer.
> >
> > I am not able to find an example for my problem in the documentation
> > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
> >
> > Would anyone had some tips to build the Fsgd file and the contrast file ?
> >
> > Thank you very much in advance.
> >
> > Best,
> >
> > Charles
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the 

Re: [Freesurfer] group analysis

[Douglas N Greve]

This is a straightforward extension to the FSGD examples. You have 3 
discrete factors (2 diagnosis, 2 gender, 6 centers), this yields 
2*2*6=24 classes. With one covariate, you would have 24 covariate 
regressors (one for each class) for a total of 48. You would then need 
to create a contrast matrix that tests for an interaction between 
diagnosis and age which is also a straight-forward extension to the 
examples.

Having said that, I think that 48 regressors is a lot unless you have 
about 500 subjects. It is also possible to have a less agressive model 
and just have two regressors, one for each diagnosis. But you'd have to 
create the design matrix yourself as this is outside of the FSGD 
specification.


On 10/05/2016 09:22 AM, charles laidi wrote:
> Dear FreeSurfers,
>
> I would like to study the interaction between age and cortical 
> thickness in patients and controls.
> My hypothesis is that there is an interaction and that cortical 
> thickness is decreasing faster with age in patients than in controls.
> I have both Male and Female included in 6 different centers.
> I would like to consider also Gender and Site (6 centers) as confounds.
>
> My understanding is that I should perform a surface based group 
> analysis with freesurfer.
>
> I am not able to find an example for my problem in the documentation 
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
>
> Would anyone had some tips to build the Fsgd file and the contrast file ?
>
> Thank you very much in advance.
>
> Best,
>
> Charles
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] group analysis

[Trisanna Sprung-Much]

there is a tutorial with similar variables available here

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Wed, Oct 5, 2016 at 9:22 AM, charles laidi 
wrote:

> Dear FreeSurfers,
>
> I would like to study the interaction between age and cortical thickness
> in patients and controls.
> My hypothesis is that there is an interaction and that cortical thickness
> is decreasing faster with age in patients than in controls.
> I have both Male and Female included in 6 different centers.
> I would like to consider also Gender and Site (6 centers) as confounds.
>
> My understanding is that I should perform a surface based group analysis
> with freesurfer.
>
> I am not able to find an example for my problem in the documentation
> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V
>
> Would anyone had some tips to build the Fsgd file and the contrast file ?
>
> Thank you very much in advance.
>
> Best,
>
> Charles
>
>
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>
>
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> HelpLine at
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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[Freesurfer] group analysis

[charles laidi]

Dear FreeSurfers,

I would like to study the interaction between age and cortical thickness in
patients and controls.
My hypothesis is that there is an interaction and that cortical thickness
is decreasing faster with age in patients than in controls.
I have both Male and Female included in 6 different centers.
I would like to consider also Gender and Site (6 centers) as confounds.

My understanding is that I should perform a surface based group analysis
with freesurfer.

I am not able to find an example for my problem in the documentation
https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G0V

Would anyone had some tips to build the Fsgd file and the contrast file ?

Thank you very much in advance.

Best,

Charles
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] group analysis/ region of interest (ROI) approach

[Douglas N Greve]

On 08/05/2016 02:35 PM, miracoo...@gmail.com wrote:
> Hello doug,
> Should I add --label-src in addition to --label-trg or should I replace the 
> latter with the former?
It does not matter as both the source and target are fsaveage
> Thanks. Also, Just to conform, I should run mri_glmfit-sim after mri_mcsim.
correct
> Best,
> Paul
>
> Sent from my BlackBerry 10 smartphone.
>Original Message
> From: Douglas N Greve
> Sent: Friday, August 5, 2016 11:49 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Reply To: Freesurfer support list
> Subject: Re: [Freesurfer] group analysis/ region of interest (ROI) approach
>
> There are several things that need to be changed as I've indicated below
>
> On 08/01/2016 10:09 PM, miracle ozzoude wrote:
>> Thanks doug. Also, Please can you verify if this are the right codes
>> for performing ROI surface based analysis using the command line. I
>> tried to reverse the whole brain analysis tutorial with some of the
>> previous threads i read. I'm trying to mask the entorhinal and MT and
>> then perform ROI on them using GLM. Thanks a lot
>>
>> CREATE MASK USING MRI_BINARIZE
>> setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri
>> cd users/paul/desktop/ims/fsaverage/mri
>> mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz
>>
>> MERGE TO LABELS
>> cd users/paul/desktop/ims/fsaverage/label
>> mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label
>>
>> MRIS_PREPROC
>> cd users/paul/desktop/ims
>> mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas
>> thickness --out lh.filename.thickness.00.mgh
>>
>> MRI_SURF2SURF
>> mri_surf2surf --hemi lh --s fsaverage --sval
>> lh.filename.thickness.00.mgh --fwhm 10 --label-trg
>> fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh
> Add --label-src lh.2mask.label
> This will cause it to smooth only in the mask
>> GLM
>> mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods
>> --C contrastmatrix.mtx --surf fsaverage lh --label
>> fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir
>>
>> CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations
>> mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2
>> mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces
> You will need to create your own correction simulation since you have
> changed the search space. See here
> http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
>> On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve
>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> I think there is an example on the wiki in the ROI analysis
>> section. See
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
>>
>> After you run aparcstats2table, you can run mri_glmfit with
>> --table aparcstatstable instead of --y. The output folder will
>> have tables with lists of ROIs and p-values
>>
>>
>>
>> On 7/30/16 5:33 PM, miracle ozzoude wrote:
>>> Hey FreeSurfer experts,
>>> Does anyone know the steps i have to perform if I want to conduct
>>> surface based thickness analysis using GLM but with ROI approach.
>>> Thank you very much.
>>> Best,
>>> Paul
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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 Partners
>> Compliance HelpLine at
>> http://www.partners.org/complianceline . 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.
>>
>>
>>
>>
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] group analysis/ region of interest (ROI) approach

[miracooloz]

Hello doug,
Should I add --label-src in addition to --label-trg or should I replace the 
latter with the former? Thanks. Also, Just to conform, I should run 
mri_glmfit-sim after mri_mcsim.  
Best, 
Paul

Sent from my BlackBerry 10 smartphone.
  Original Message  
From: Douglas N Greve
Sent: Friday, August 5, 2016 11:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Reply To: Freesurfer support list
Subject: Re: [Freesurfer] group analysis/ region of interest (ROI) approach

There are several things that need to be changed as I've indicated below

On 08/01/2016 10:09 PM, miracle ozzoude wrote:
> Thanks doug. Also, Please can you verify if this are the right codes 
> for performing ROI surface based analysis using the command line. I 
> tried to reverse the whole brain analysis tutorial with some of the 
> previous threads i read. I'm trying to mask the entorhinal and MT and 
> then perform ROI on them using GLM. Thanks a lot
>
> CREATE MASK USING MRI_BINARIZE
> setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri
> cd users/paul/desktop/ims/fsaverage/mri
> mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz
>
> MERGE TO LABELS
> cd users/paul/desktop/ims/fsaverage/label
> mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label
>
> MRIS_PREPROC
> cd users/paul/desktop/ims
> mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas 
> thickness --out lh.filename.thickness.00.mgh
>
> MRI_SURF2SURF
> mri_surf2surf --hemi lh --s fsaverage --sval 
> lh.filename.thickness.00.mgh --fwhm 10 --label-trg 
> fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh
Add --label-src lh.2mask.label
This will cause it to smooth only in the mask
>
> GLM
> mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods 
> --C contrastmatrix.mtx --surf fsaverage lh --label 
> fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir
>
> CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations
> mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 
> mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces
You will need to create your own correction simulation since you have 
changed the search space. See here
http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
>
> On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> I think there is an example on the wiki in the ROI analysis
> section. See
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
>
> After you run aparcstats2table, you can run mri_glmfit with
> --table aparcstatstable instead of --y. The output folder will
> have tables with lists of ROIs and p-values
>
>
>
> On 7/30/16 5:33 PM, miracle ozzoude wrote:
>> Hey FreeSurfer experts,
>> Does anyone know the steps i have to perform if I want to conduct
>> surface based thickness analysis using GLM but with ROI approach.
>> Thank you very much.
>> Best,
>> Paul
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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 Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . 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.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] group analysis/ region of interest (ROI) approach

[Douglas N Greve]

There are several things that need to be changed as I've indicated below

On 08/01/2016 10:09 PM, miracle ozzoude wrote:
> Thanks doug. Also, Please can you verify if this are the right codes 
> for performing ROI surface based analysis using the command line. I 
> tried to reverse the whole brain analysis tutorial with some of the 
> previous threads i read. I'm trying to mask the entorhinal and MT and 
> then perform ROI on them using GLM. Thanks a lot
>
> CREATE MASK USING MRI_BINARIZE
> setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri
> cd users/paul/desktop/ims/fsaverage/mri
> mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz
>
> MERGE TO LABELS
> cd users/paul/desktop/ims/fsaverage/label
> mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label
>
> MRIS_PREPROC
> cd users/paul/desktop/ims
> mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas 
> thickness --out lh.filename.thickness.00.mgh
>
> MRI_SURF2SURF
> mri_surf2surf --hemi lh --s fsaverage --sval 
> lh.filename.thickness.00.mgh --fwhm 10 --label-trg 
> fsaverage/label/lh.2mask.label --tval lh.filename.thickness.10B.mgh
Add --label-src lh.2mask.label
This will cause it to smooth only in the mask
>
> GLM
> mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods 
> --C contrastmatrix.mtx --surf fsaverage lh --label 
> fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir
>
> CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations
> mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 
> mc-z.positive --sim-sign pos --cwpvalthresh 0.05 --2spaces
You will need to create your own correction simulation since you have 
changed the search space. See here
http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
>
> On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve 
> > wrote:
>
> I think there is an example on the wiki in the ROI analysis
> section.  See
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
>
> After you run aparcstats2table, you can run mri_glmfit with
> --table aparcstatstable instead of --y. The output folder will
> have tables with lists of ROIs and p-values
>
>
>
> On 7/30/16 5:33 PM, miracle ozzoude wrote:
>> Hey FreeSurfer experts,
>> Does anyone know the steps i have to perform if I want to conduct
>> surface based thickness analysis using GLM but with ROI approach.
>> Thank you very much.
>> Best,
>> Paul
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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 Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . 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.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] group analysis/ region of interest (ROI) approach

[miracle ozzoude]

Thanks doug. Also, Please can you verify if this are the right codes for
performing ROI surface based analysis using the command line. I tried to
reverse the whole brain analysis tutorial with some of the previous threads
i read. I'm trying to mask the entorhinal and MT and then perform ROI on
them using GLM. Thanks a lot

CREATE MASK USING MRI_BINARIZE
setenv SUJECTS_DIR users/paul/desktop/ims/fsaverage/mri
cd users/paul/desktop/ims/fsaverage/mri
mri_binarize --match [subjects] -i aparc+aseg.mgz -o lh.2mask.mgz

MERGE TO LABELS
cd users/paul/desktop/ims/fsaverage/label
mri_mergelabels -i lh.entorhinal.label -i lh.MT.label -o lh.2mask.label

MRIS_PREPROC
cd users/paul/desktop/ims
mris_preproc -fsgd filename.fsgd --target fsaverage hemi lh --meas
thickness --out lh.filename.thickness.00.mgh

MRI_SURF2SURF
mri_surf2surf --hemi lh --s fsaverage --sval lh.filename.thickness.00.mgh
--fwhm 10 --label-trg fsaverage/label/lh.2mask.label --tval
lh.filename.thickness.10B.mgh

GLM
mri_glmfit --y lh.filename.thickness.10B.mgh --fsgd filname.fsgd dods --C
contrastmatrix.mtx --surf fsaverage lh --label
fsaverage/label/lh.2mask.label --glmdir lh.filename.glmdir

CORRECTING FOR MULTIPLE COMPARISONS WITH MONTE CARLO 5000 iterations
mri_glmfit-sim --glmdir lh.firstscore.glmdir --sim mc-z 5 2 mc-z.positive
--sim-sign pos --cwpvalthresh 0.05 --2spaces

On Mon, Aug 1, 2016 at 9:50 PM, Douglas Greve 
wrote:

> I think there is an example on the wiki in the ROI analysis section.  See
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI
>
> After you run aparcstats2table, you can run mri_glmfit with --table
> aparcstatstable instead of --y. The output folder will have tables with
> lists of ROIs and p-values
>
>
>
> On 7/30/16 5:33 PM, miracle ozzoude wrote:
>
> Hey FreeSurfer experts,
> Does anyone know the steps i have to perform if I want to conduct surface
> based thickness analysis using GLM but with ROI approach. Thank you very
> much.
> Best,
> Paul
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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 Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . 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.
>
>
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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 Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] group analysis/ region of interest (ROI) approach

[Douglas Greve]

I think there is an example on the wiki in the ROI analysis section.  See

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

After you run aparcstats2table, you can run mri_glmfit with --table 
aparcstatstable instead of --y. The output folder will have tables with 
lists of ROIs and p-values




On 7/30/16 5:33 PM, miracle ozzoude wrote:

Hey FreeSurfer experts,
Does anyone know the steps i have to perform if I want to conduct 
surface based thickness analysis using GLM but with ROI approach. 
Thank you very much.

Best,
Paul


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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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.

[Freesurfer] group analysis/ region of interest (ROI) approach

[miracle ozzoude]

Hey FreeSurfer experts,
Does anyone know the steps i have to perform if I want to conduct surface
based thickness analysis using GLM but with ROI approach. Thank you very
much.
Best,
Paul
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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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . 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.