Hi Doug,
Thanks for the fast respons.
I did the correction for multiple comparisons with the following configurations: abs, z=1.3 (p<0.05). Is the output from mri_glmfit-sim in the command line the same as the correction for multiple comparisons in qdec? is the file xxx.y.ocn.dat created after multiple comparisons simulations in qdec?
The problem is where can i find the xxx.y.ocn.dat file? in which directory?
I did not find the file in the (group comparison) output directory called Pd_vs_HC_1 or in the subdirectories of the directory Pd_vs_HC_1 lh-Diff-1.00-2.00-Intercept-thickness or the other subdirectory lh-Avg-Intercept-thickness
Many thanks,
Stan
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 14 January 2013 16:40 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mean cluster thickness in qdec
Stan, QDEC will create an output directory (the "glmdir"). This is actually created by mri_glmfit which is run by QDEC. If you did not run mri_glmfit-sim from QDEC, you can run it from the command line. To get help, run mri_glmfit-sim --help. The file you want is xxx.y.ocn.dat (help section for this is below)
doug
csdbase.y.ocn.dat - this is a summary of the input (y) over each cluster. It has a column for each cluster. Each row is a subject. The value is the average of the input (y) in each cluster. This is a simple text file.
On 01/14/2013 09:08 AM, Berg, S.F. van den wrote:
Dear Freesurfer Experts,
I would like the mean thickness measures of each cluster i found in qdec.
I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I found 5 different significant clusters. I would like to extract the mean cortical thickness of each significant cluster in the patient group and in the healthy control group. If this is not possible the mean cortical thickness of the peak/max vertex is also enough information. Where can i found the file with this information?
the problem is what do i have to do? run mri_glmfit-sim? but qdec do not create a .glmdir file? so do i have to run the mri_glmfit first? or is mri_glmfit-sim enough but where is the .glmdir file?
I use mri_glmfit-sim --glmdir ?.glmdir --sim mc-z 10000 1.3 mc-z.negative --sim-sign abs --cwpvalthresh 0.5 --overwrite
I want to create the csdbase.y.ocn.dat (explaind in mri_glmfit-sim --help) for the mean cluster thickness. This is the file where i can find the mean thickness of each cluster, right?
A jpeg file is attached to this email.
Many thanks,
Stan
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