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From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
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
: [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 :
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9
I have attached three of the output summary files
Can you please confirm how to assess
: Re: [Freesurfer] qdec analysis with 2 covariates
Yes, with a 95% confidence range of .7962 to .8065
doug
On 12/17/2013 11:04 AM, Jon Wieser wrote:
so in the following cluster, the cluster-wise p-value is 0.80130?
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow
: 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 :
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cache 2.0 abs --cwp .9
I have attached three of the output summary files
Can you please confirm how
Wieser wie...@uwm.edu, 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
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu, 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
@nmr.mgh.harvard.edu
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
window when you see 40 clusters? It might be that it is showing clusters
regardless of the cluster
freesurfer@nmr.mgh.harvard.edu
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
gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
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
: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
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
: [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 recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99
ERROR: Flag --cwd unrecognized.
--glmdir MTA_ADHD_MJ --cwd .99
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 recognize the --cwd option
mri_glmfit-sim --glmdir MTA_ADHD_MJ --cwd .99
ERROR: Flag --cwd unrecognized.
--glmdir MTA_ADHD_MJ --cwd .99
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Monday, December 9, 2013 5:02:41 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
which file did you look in? It should have a name like
cache.th20.abs.y.ocn.dat
On 12/09/2013 05:09 PM, Jon Wieser wrote:
I found data
...@uwm.edu, 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:
i was getting the values for the command
: Re: [Freesurfer] qdec analysis with 2 covariates
Is there a cache.mri_glmfit-sim.log in the output folder? Can you send
it to me? Also, please remember to post to the list. thanks!
doug
On 12/10/2013 02:30 PM, Jon Wieser wrote:
FS version 5.3
- Original Message -
From: Douglas N
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
Is there a cache.mri_glmfit-sim.log in the output folder? Can you send
it to me? Also, please remember to post to the list. thanks!
doug
On 12/10/2013 02:30 PM, Jon Wieser wrote:
FS version 5.3
- Original Message -
From
...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
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
, 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 means that you
will have to run mri_glmfit-sim yourself, something like
mri_glmfit
@nmr.mgh.harvard.edu
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 means that you
will have to run mri_glmfit-sim yourself
...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
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
want?
On 12/10/2013 04:37 PM
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
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 but the
y.ocn.dat file only has a few columns?
On 12
: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu, 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
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 with
...@nmr.mgh.harvard.edu
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
of thickness data , for feach subject in the analysis
Jon
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
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
: freesurfer freesurfer@nmr.mgh.harvard.edu
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
to that data?
Jon
- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Jon Wieser wie...@uwm.edu
Cc: freesurfer freesurfer@nmr.mgh.harvard.edu
Sent: Monday, December 9, 2013 2:15:39 PM
Subject: Re: [Freesurfer] qdec analysis with 2 covariates
It is in one of the output
HI freesurfer experts
I want to do an analysis in qdec with 2 groups(ADHD, and Marijuana usage) and
2 covariates(age and gender) to study the effect of these factors on cortical
thickness. I can only select a covariate in the qdec gui. is there a way to
select both covariates in the qdec
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