[Freesurfer] normalizing in fsgd

2016-07-24 Thread miracle ozzoude 
Hello freesurfer experts,
I am trying to normalize my continuous variables in my fsgd file. Is this
the correct term to add to my fsgd file in order for mri_glmfit to
normalize it?

GroupDescriptorFile 1
Title PCS
Class group1
Class group2
Normalize 1
Variables Age Education Scoreone Scoretwo
Input 053 group1 47 18 3.4 5.6
Input 054 group2 50 16 5.3 2.8

Thank you,
Paul
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Re: [Freesurfer] normalizing in fsgd

2016-07-25 Thread Douglas Greve 
No, that flag does not exist, but it is a good idea! You'll have to 
normalize them by hand.



On 7/24/16 1:33 PM, miracle ozzoude wrote:

Hello freesurfer experts,
I am trying to normalize my continuous variables in my fsgd file. Is 
this the correct term to add to my fsgd file in order for mri_glmfit 
to normalize it?


GroupDescriptorFile 1
Title PCS
Class group1
Class group2
Normalize 1
Variables Age Education Scoreone Scoretwo
Input 053 group1 47 18 3.4 5.6
Input 054 group2 50 16 5.3 2.8

Thank you,
Paul


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Re: [Freesurfer] normalizing in fsgd

2016-07-25 Thread Douglas Greve 
Actually, I checked the code and found that I had already put a flag in 
there to do this (I'm so clever). Add


ReScaleFlag 1

in addition to

DeMeanFlag 1




On 7/25/16 11:22 AM, Douglas Greve wrote:


No, that flag does not exist, but it is a good idea! You'll have to 
normalize them by hand.



On 7/24/16 1:33 PM, miracle ozzoude wrote:

Hello freesurfer experts,
I am trying to normalize my continuous variables in my fsgd file. Is 
this the correct term to add to my fsgd file in order for mri_glmfit 
to normalize it?


GroupDescriptorFile 1
Title PCS
Class group1
Class group2
Normalize 1
Variables Age Education Scoreone Scoretwo
Input 053 group1 47 18 3.4 5.6
Input 054 group2 50 16 5.3 2.8

Thank you,
Paul


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Re: [Freesurfer] normalizing in fsgd

2016-07-26 Thread miracle ozzoude 
Hello Doug,
The ReScaleFlag 1 command did not work. Only the demean command.
Paul


On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve 
wrote:

> Actually, I checked the code and found that I had already put a flag in
> there to do this (I'm so clever). Add
>
> ReScaleFlag 1
>
> in addition to
>
> DeMeanFlag 1
>
>
>
>
> On 7/25/16 11:22 AM, Douglas Greve wrote:
>
> No, that flag does not exist, but it is a good idea! You'll have to
> normalize them by hand.
>
> On 7/24/16 1:33 PM, miracle ozzoude wrote:
>
> Hello freesurfer experts,
> I am trying to normalize my continuous variables in my fsgd file. Is this
> the correct term to add to my fsgd file in order for mri_glmfit to
> normalize it?
>
> GroupDescriptorFile 1
> Title PCS
> Class group1
> Class group2
> Normalize 1
> Variables Age Education Scoreone Scoretwo
> Input 053 group1 47 18 3.4 5.6
> Input 054 group2 50 16 5.3 2.8
>
> Thank you,
> Paul
>
>
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>
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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
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> properly
> dispose of the e-mail.
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Re: [Freesurfer] normalizing in fsgd

2016-07-26 Thread Douglas N Greve 
what do you mean it did not work? can you be more specific?


On 07/26/2016 12:21 PM, miracle ozzoude wrote:
> Hello Doug,
> The ReScaleFlag 1 command did not work. Only the demean command.
> Paul
>
>
> On Mon, Jul 25, 2016 at 6:17 PM, Douglas Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Actually, I checked the code and found that I had already put a
> flag in there to do this (I'm so clever). Add
>
> ReScaleFlag 1
>
> in addition to
>
> DeMeanFlag 1
>
>
>
>
> On 7/25/16 11:22 AM, Douglas Greve wrote:
>>
>> No, that flag does not exist, but it is a good idea! You'll have
>> to normalize them by hand.
>>
>>
>> On 7/24/16 1:33 PM, miracle ozzoude wrote:
>>> Hello freesurfer experts,
>>> I am trying to normalize my continuous variables in my fsgd
>>> file. Is this the correct term to add to my fsgd file in order
>>> for mri_glmfit to normalize it?
>>>
>>> GroupDescriptorFile 1
>>> Title PCS
>>> Class group1
>>> Class group2
>>> Normalize 1
>>> Variables Age Education Scoreone Scoretwo
>>> Input 053 group1 47 18 3.4 5.6
>>> Input 054 group2 50 16 5.3 2.8
>>>
>>> Thank you,
>>> Paul
>>>
>>>
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>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> 
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
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>
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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
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> sender and properly
> dispose of the e-mail.
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Re: [Freesurfer] normalizing in fsgd

2016-07-26 Thread miracle ozzoude 
I added normalizing and demeaning code like you suggested in my fsgd file
and perform the GLM analysis (mri_glmfit). However, my covariates were only
demeaned (DeMeanFlag 1) but they were not normalized (ReScaleFlag 1). Hence
I received this error from freesurfer. I have attached my fsgd files and
contrast matrix
INFO: demeaning continuous variables
Continuous Variable Means (all subjects)
0 Age 39.9375 17.3312
1 Education 15.5625 1.99902
2 Firstscore 1.03375 0.341785
3 Secondscore 1.03906 0.370678
4 Thirdscore 1.13844 0.4768
5 Averagescore 1.07375 0.364046
Class Means of each Continuous Variable
1 Group1  35.6316  15.0526   1.0342   1.2111   1.4289   1.2305
2 Group2  46.2308  16.3077   1.0331   0.7877   0.7138   0.8446
INFO: gd2mtx_method is dods
Reading source surface
/Users/ctartaglia/Desktop/improvervsdeclinermri/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea   0.399267
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $
cwd /Users/ctartaglia/Desktop/improvervsdeclinermri
cmdline mri_glmfit --y lh.NeuroTrackerscore.thickness.10B.mgh --fsgd
NeuroTrackerscore.fsgd dods --C new.firstmatrix.mtx --C
new.secondmatrix.mtx --C new.thirdmatrix.mtx --C new.fourthmatrix.mtx --C
new.fifthmatrix.mtx --C new.sixthmatrix.mtx --C new.seventhmatrix.mtx --C
new.eightmatrix.mtx --C new.ninethmatrix.mtx --C new.tenthmatrix.mtx --surf
fsaverage lh --cortex --glmdir lh.NeuroTrackerscore.glmdir
sysname  Darwin
hostname twh-ct-lab4-imac.uhn.ca
machine  x86_64
user ctartaglia
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Users/ctartaglia/Desktop/improvervsdeclinermri/lh.NeuroTrackerscore.thickness.10B.mgh
logyflag 0
usedti  0
FSGD NeuroTrackerscore.fsgd
labelmask
/Users/ctartaglia/Desktop/improvervsdeclinermri/fsaverage/label/lh.cortex.label
maskinv 0
glmdir lh.NeuroTrackerscore.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory lh.NeuroTrackerscore.glmdir
Loading y from
/Users/ctartaglia/Desktop/improvervsdeclinermri/lh.NeuroTrackerscore.thickness.10B.mgh
INFO: gd2mtx_method is dods
Saving design matrix to lh.NeuroTrackerscore.glmdir/Xg.dat
Normalized matrix condition is 115605
Design matrix --
 1.000   0.000  -0.729   0.000  -0.026   0.000   1.889   0.000   1.535
0.000   1.428   0.000   1.729   0.000;
 1.000   0.000   0.425   0.000   0.474   0.000  -0.568   0.000  -0.866
0.000  -0.501   0.000  -0.716   0.000;
 1.000   0.000   0.194   0.000   0.974   0.000  -0.715   0.000  -1.001
0.000  -0.438   0.000  -0.771   0.000;
 1.000   0.000  -0.960   0.000  -1.027   0.000  -0.568   0.000  -0.408
0.000  -0.354   0.000  -0.496   0.000;
 1.000   0.000  -0.440   0.000  -1.027   0.000   0.075   0.000  -0.246
0.000  -0.124   0.000  -0.139   0.000;
 1.000   0.000  -0.440   0.000   1.474   0.000  -0.188   0.000   0.132
0.000  -0.208   0.000  -0.111   0.000;
 1.000   0.000   0.079   0.000   0.474   0.000  -0.480   0.000  -0.165
0.000  -0.124   0.000  -0.276   0.000;
 1.000   0.000  -0.902   0.000  -0.527   0.000  -0.100   0.000   0.429
0.000   0.044   0.000   0.108   0.000;
 1.000   0.000   1.291   0.000   0.474   0.000  -0.188   0.000  -0.246
0.000  -0.040   0.000   0.108   0.000;
 1.000   0.000  -0.440   0.000   1.474   0.000  -0.480   0.000  -0.569
0.000  -0.900   0.000  -0.743   0.000;
 1.000   0.000   0.598   0.000   0.474   0.000  -0.773   0.000  -0.408
0.000   0.317   0.000  -0.249   0.000;
 1.000   0.000  -0.844   0.000   0.474   0.000   1.597   0.000   1.535
0.000   0.736   0.000   1.317   0.000;
 1.000   0.000  -0.787   0.000   0.474   0.000   1.363   0.000   0.024
0.000   0.422   0.000   0.603   0.000;
 1.000   0.000  -0.960   0.000  -1.027   0.000   1.480   0.000   1.265
0.000   1.428   0.000   1.509   0.000;
 1.000   0.000  -1.075   0.000  -1.527   0.000  -0.100   0.000  -0.327
0.000  -0.270   0.000  -0.276   0.000;
 1.000   0.000   0.887   0.000   0.474   0.000  -0.276   0.000   0.887
0.000   0.527   0.000   0.438   0.000;
 1.000   0.000   0.483   0.000   0.474   0.000   0.544   0.000   0.240
0.000   0.149   0.000   0.301   0.000;
 1.000   0.000   2.445   0.000  -1.527   0.000  -1.241   0.000  -0.246
0.000  -0.585   0.000  -0.743   0.000;
 1.000   0.000   1.175   0.000  -1.027   0.000  -1.270   0.000  -1.568
0.000  -1.508   0.000  -1.595   0.000;
 0.000   1.000   0.000   0.217   0.000   0.847   0.000   0.254   0.000
0.411   0.000   0.474   0.000   0.427;
 0.000   1.000   0.000  -1.513   0.000  -0.654   0.000   0.254   0.000
0.141   0.000  -0.239   0.000   0.015;
 0.000   1.000   0.000   0.102   0.000  -0.154   0.000  -1.764   0.000
-1.181   0.000  -0.763   0.000  -1.276;
 0.000   1.000   0.000  -1.340   0.000  -0.154   0.000   1.600   0.000
1.166   0.000   1.062   0.000   1.361;
 0.000   1.000   0.000  -1.687   0.000   0.346   0.000   1.366   0.000
1.274   0.000   0.999   0.000   1.306;
 0.000   1.000   0.000   0.275   0.000   0.847