ery insignificant. Am I missing
> somthing?
> Jon
>
> - Original Message -
> From: "Douglas N Greve"
> To: "Jon Wieser"
> Cc: "freesurfer"
> Sent: Tuesday, December 17, 2013 10:46:36 AM
> Subject: Re: [Freesurfer] qdec analysis with
I would think that a p-value of 0.8013 is very insignificant. Am I missing
somthing?
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Tuesday, December 17, 2013 10:46:36 AM
Subject: Re: [Freesurfer] qdec analysis w
3.247 90900134.66-37.1 -33.2 -24.5 0.80130 0.79620
> 0.80640 267 fusiform
>
>
> - Original Message -
> From: "Douglas N Greve"
> To: "Jon Wieser"
> Cc: "freesurfer"
> Sent: Monday, December 16, 2013 4
-
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Monday, December 16, 2013 4:28:30 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
look at the CWP column
doug
On 12/16/2013 05:14 PM, Jon Wieser wrote:
> Hi Doug
>
> I ran
er-wise p-value?
>
> Jon
>
> - Original Message -
> From: "Douglas N Greve"
> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu
> Sent: Friday, December 13, 2013 12:12:01 PM
> Subject: Re: [Freesurfer] qdec analysis with 2 covariates
>
>
r" , Freesurfer@nmr.mgh.harvard.edu
Sent: Friday, December 13, 2013 12:12:01 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
I would have thought that it would have gotten all of them. You can try
something like --cwp .9
On 12/13/2013 01:03 PM, Jon Wieser wrote:
> HI doug
n the GUI.
> perhaps theses are the most significant clusters?
> Jon
>
> - Original Message -
> From: "Douglas N Greve"
> To: "Jon Wieser"
> Cc: "freesurfer"
> Sent: Friday, December 13, 2013 11:43:29 AM
> Subject: Re: [Freesurfer] qdec
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99
>> ERROR: Flag --cwd unrecognized.
>> --glmdir MTA_ADHD_MJ --cwd .99
>>
>>
>>
>>
>>
>>
>> - Original Message -
>> From: "Douglas N Greve"
>> To: "Jon Wieser"
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Friday, December 13, 2013 11:18:49 AM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
sorry, it is --cwp
On 12/13/2013 12:12 PM, Jon Wieser wrote:
> HI Doug
> MRI_glmfit-sim didn't rec
;
>
> - Original Message -
> From: "Douglas N Greve"
> To: "Jon Wieser"
> Cc: "freesurfer"
> Sent: Friday, December 13, 2013 10:54:19 AM
> Subject: Re: [Freesurfer] qdec analysis with 2 covariates
>
>
> I'm sure that those clu
t;
Sent: Friday, December 13, 2013 10:54:19 AM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
I'm sure that those clusters are not very significant. Try running
mri_glmfit-sim with --cwd .99 to capture all clusters
doug
On 12/12/2013 03:27 PM, Jon Wieser wrote:
> HI Doug,
&
: "Douglas N Greve"
> To: "Jon Wieser"
> Cc: "freesurfer"
> Sent: Thursday, December 12, 2013 1:15:58 PM
> Subject: Re: [Freesurfer] qdec analysis with 2 covariates
>
>
> I'm not sure what is going on. Can you send a screen shot of the qdec
> w
"
Sent: Thursday, December 12, 2013 1:22:35 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
It is showing you scatter plots from individual vertices, not an average
over the cluster
doug
On 12/12/2013 12:27 PM, Jon Wieser wrote:
> Is it possible to get the individual subjec
output the data values
> used to make the graph?
> Jon
>
> - Original Message -
> From: "Jon Wieser"
> To: "Douglas N Greve"
> Cc: "freesurfer"
> Sent: Tuesday, December 10, 2013 4:32:10 PM
> Subject: Re: [Freesurfer] qdec analysis
der as covariates
> Jon
>
> Jon
> - Original Message -
> From: "Douglas N Greve"
> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu
> Sent: Tuesday, December 10, 2013 4:20:30 PM
> Subject: Re: [Freesurfer] qdec analysis with 2 covariates
&g
ble.dat file
we are also looking at age and gender as covariates
Jon
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 10, 2013 4:20:30 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
From: "Douglas N Greve"
To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu
Sent: Tuesday, December 10, 2013 4:20:30 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
which contrast are you looking at in QDEC? Also, what is the voxel-wise
threshold in QDEC? The va
> From: "Douglas N Greve"
> To: "Jon Wieser"
> Cc: "freesurfer"
> Sent: Tuesday, December 10, 2013 4:03:06 PM
> Subject: Re: [Freesurfer] qdec analysis with 2 covariates
>
>
> So one of the contrasts has 40 clusters in the summary file
;Douglas N Greve"
> To: "Jon Wieser"
> Cc: "freesurfer"
> Sent: Tuesday, December 10, 2013 3:44:50 PM
> Subject: Re: [Freesurfer] qdec analysis with 2 covariates
>
>
> There should be a column for each cluster in contrast. Is that what you
> w
yes, that is what we want, but the files contain only 1-3 columns
Jon
- Original Message -
From: "Douglas N Greve"
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Tuesday, December 10, 2013 3:44:50 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
each cluster, for every subject
>
> we have 120 subjects, with about 40 clusters
> Jon
>
> - Original Message -
> From: "Douglas N Greve"
> To: "Jon Wieser"
> Cc: "freesurfer"
> Sent: Tuesday, December 10, 2013 2:30:31 PM
> Subject:
To: "Jon Wieser"
Cc: "freesurfer"
Sent: Tuesday, December 10, 2013 2:30:31 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
OK, sorry, I thought qdec was running a script called mri_glmfit-sim but
it appears to be running the correction internally. That me
te:
>> FS version 5.3
>>
>> - Original Message -
>> From: "Douglas N Greve"
>> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu
>> Sent: Tuesday, December 10, 2013 1:05:26 PM
>> Subject: Re: [Freesurfer] qdec analysis with 2 cov
t;Douglas N Greve"
> To: "Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu
> Sent: Tuesday, December 10, 2013 1:05:26 PM
> Subject: Re: [Freesurfer] qdec analysis with 2 covariates
>
>
> hmmm, it should be there. What version of FS are you using?
>
>
>
> On
"Jon Wieser" , Freesurfer@nmr.mgh.harvard.edu
> Sent: Tuesday, December 10, 2013 1:05:26 PM
> Subject: Re: [Freesurfer] qdec analysis with 2 covariates
>
>
> hmmm, it should be there. What version of FS are you using?
>
>
>
> On 12/10/2013 12:57 PM, Jon Wieser wrote
.00 0.000100 0.000287 36.918144
> 0.00 0.715900
>98 1726.007812 0.00 0.000100 0.000259 37.273422
> 0.00 0.715900
>99 1741.530029 0.000100 -0.000000 0.000234 37.628700
> 0.715900 0.00
>
> - Orig
> direct me to that data?
> Jon
> - Original Message -
> From: "Douglas N Greve"
> To: "Jon Wieser"
> Cc: "freesurfer"
> Sent: Monday, December 9, 2013 2:15:39 PM
> Subject: Re: [Freesurfer] qdec analysis with 2 covariates
>
>
eesurfer"
Sent: Monday, December 9, 2013 2:15:39 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
It is in one of the output files. Look for the .dat file in
mri_glmfit-sim --help
On 12/09/2013 03:01 PM, Jon Wieser wrote:
> thanks doug,
>
> We've run a 2x2 analy
> How can i get a table of thickness data , for feach subject in the analysis
> Jon
>
> - Original Message -
> From: "Douglas N Greve"
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Monday, December 9, 2013 1:48:15 PM
> Subject: Re: [Freesurfer] qdec analysis with
To: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, December 9, 2013 1:48:15 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
Hi Jon, QDEC does not currently allow more than one covariates of
interest. You will have to use the command-line stream (ie,
mris_preproc, mri_surf2surf, mri_glm
Hi Jon, QDEC does not currently allow more than one covariates of
interest. You will have to use the command-line stream (ie,
mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim)
doug
On 12/05/2013 02:57 PM, Jon Wieser wrote:
> HI freesurfer experts
>
> I want to do an analysis in qdec wi
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