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 greve@nmr.mgh.harvard.edu To: Antonella Kis atorok9@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:
- 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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