Dear Doug,
Thank you very much for your valuable reply.
I still have few questions on which I would like to ask your advise:
QUESTION 1:
While running the recall-all for all my subjects I also used the -qcache
option. I am not sure how this data is further used for my GLM analysis.
I will appreciate if you can confirm if in this case in order to do a
thickness-age correlation group study I need to complete the following steps:
STEP 1: Uncached Data: resamples each subjects data to fsaveragea (into a
common space), and Concatenating all the subjects' into a single file by running
mris_preproc --fsgd AGE_fsgd.fsgd \
--target fsaverage --hemi lh \
--meas thickness \
--out lh.AGE.thickness.00.mgh
STEP 2: The independent variable is the thickness smoothed at various FWHM
(full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm so run:
mris_preproc --fsgd AGE_fsgd.fsgd \
--cache-in thickness.fwhm10.fsaverage \
--target fsaverage --hemi lh \
--out lh.AGE.thickness.10.mgh
STEP 3: If I run the next step (I know is optional) where I can use this data
lh.AGE.thickness.10B.mgh? Is this a better data to be use for my further steps?
OPTIONAL: THIS WILL TAKE ABOUT 5 MINUTES
mri_surf2surf --hemi lh \
--s fsaverage \
--sval lh.AGE.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.AGE.thickness.10B.mgh
STEP 4: GLM Analysis (mri_glmfit)
mri_glmfit \
--y lh.AGE.thickness.10.mgh \
--fsgd AGE_fsgd.fsgd dods\
--C lh-Avg-thickness-age-Cor.mtx \
--surf fsaverage lh \
--cortex \
--glmdir lh.AGE.glmdir
STEP 5: View the uncorrected significance map with tksurfer:
tksurfer fsaverage lh inflated \
-annot aparc.annot -fthresh 2 \
-overlay lh.AGE.glmdir/lh-Avg-thickness-age-Cor/sig.mgh
STEP 6: Viewing the medial surface, change the overlay threshold to something
very, very low (say, .01), View --> Configure --> Overlay, set "Min" .01
STEP 7: CSD (Cluster Simulation Data)- Run the Simulation
mri_glmfit-sim \
--glmdir lh.AGE.glmdir \
--sim mc-z 5 4 mc-z.negative \
--sim-sign neg \
--overwrite
QUESTION 2: You mentioned that I should use the --cache option to
mri_glmfit-sim. How I should do this? Do I need to change STEP 7?
QUESTION 3: How I can check my data to make sure that I have actual
activation above the voxel-wise threshold and how I can change my threshold?
Based on what I need to change my threshold? Do I change my treshold until I
find some activation?
Thank you very much for your valuable help.
Antonella
________________________________
From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
To: Antonella Kis <ator...@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, August 16, 2011 12:04 PM
Subject: Re: [Freesurfer] thickness-age correlation
Antonella Kis wrote:
> Dear Freesurfer experts,
>
> I am doing a thickness-age correlation group difference study (patients
> versus controls. I would like to know if:
>
> 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the
> change in thickness with age
>
Yes.
> 2)what is the best iteration number for the simulation? Should be 5000 or
> 1000 or greater?
>
10,000 -- note that if you're doing a whole-hemisphere correction with the
monte-carlo simulation then you should use the pre-computed results (use the
--cache option to mri_glmfit-sim)
> 3)why when I run the simulation for 5 iterations I've got zero clusters?
>
You should look at your data to make sure that you have actual activation above
the voxel-wise threshold you have set. Also, only 5 clusters would not be
enough to get a significant cluster anyway.
> 4)can I derive the thickness from the significant clusters of glm analysis?
> Do I need to run QDEC after GLM?
>
If you mean that you want the average thickness from each subject for a given
cluster, then this information is generated with mri_glmfit-sim in the
csdbase.y.ocn.dat file.
doug
> Thanks for any enlightenment.
> Antonella
>
> ------------------------------------------------------------------------
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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