Hi Doug,
Thanks again for your valuable help. I followed your suggestions but to better understand my results and the analysis of my data I have few more questions:
1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get more clusters than the number of clusters obtained from mri_glmfit-sim?
2). What sig.mgh represents?
3) What's the real significance of a cluster (how a cluster is formed) obtained by mri_glmfit-sim?
4). Should my ROI's be defined or be the same with my clusters?
5). What is the difference between GLM and Qdec?
6). Which one is the best GLM or Qdec in order to analyse the relation between age and cortical thickness for my patients versus control group?
7). Why when analysing with Qdec I get more clusters (I've got 41 for Min treshold = 2 and Max = 5 while using GLM with a threshold of 2 I've got 8 clusters)?
8). Are this clusters representing or identical with the sig.mgh as in GLM? The spots/clusters in Qdec are very similar with the sig.mgh image in GLM.
9). When using Qdec I can find as an output the number of clusters in the terminal but how I can get the cortical thickness values that corresponds to this clusters ?
Thank you very much for your time and 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: Monday, August 22, 2011 12:00 PM Subject: Re: [Freesurfer] mri_glmfit-sim
You should run mri_glmfit-sim as described in the tutorial and slides on line. This will correct for multiple comparisons. You can report the clusters that survive (if any). doug
Antonella Kis wrote:
Dear Doug,
I will be very grateful if you can advise me with the following issue: if I finished running the GLM what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my patients versus control group. Should I check only within the formed clusters? How should analyse my data after completing the GLM? Should I use visualize and plotting and in this case should I load the clusters as my ROI? I am very confused and I have no clue how to further analyse my data.
THANK YOU VERY MUCH! 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:* Thursday, August 18, 2011 1:09 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim
No you don't. This is the reason I wrote mri_glmfit-sim -- so you don't need to specify things that it can figure out automatically. doug
Antonella Kis wrote:
Hi Doug,
When I run the:
mri_glmfit-sim \ --glmdir lh.age.glmdir \ --cache 4 neg \ --overwrite
do I need to specify the --fwhm and/or to use the residual fwhm obtained from the y.fsgd file? If not when I have to input this value during my GLM analysis?
Thank you. Antonella
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> *To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com> *Cc:* "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> *Sent:* Wednesday, August 17, 2011 1:10 PM *Subject:* Re: [Freesurfer] mri_glmfit-sim
Antonella Kis wrote:
Hi Doug,
Thanks again for your help. There are few more things not very clear for me and I will be very graetful if you can advise me:
1). Did you mean that if I did not qcache my data while I was doing pre-processing running the recon-all I should use then lh.AGE.thickness.10B.mgh?
yes
- Are then the mentioned steps the right one to be followed?
yes
- I saw on one tutorial about the mri_glm to perform estimations.
What are this estimations? Do I need to run:
Where did you see reference to mris_glm? This is an old program that we should not even distribute.
# For the left hemisphere mris_glm --surfmeas thickness \ --hemi lh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100lh.mgz\ --var ./var_doss-thickness-100lh.mgz \ --y ./y_doss-thickness-100lh_000.mgz \ --nsmooth 100 # For the right hemisphere mris_glm --surfmeas thickness \ --hemi rh \ --trgsubj average \ --fsgd ./my_gender_age_fsgd.txt doss \ --beta ./beta_doss-thickness-100rh.mgz \ --var ./var_doss-thickness-100rh.mgz \ --y ./y_doss-thickness-100rh_000.mgz \ --nsmooth 100 4) If I have less than 80 subjects do I need to run the full MC simulation and I must supply the smoothest of my data as fwhm from the y.fsgd file? Also I would need to mention the threshold like in the following example?
Yes. You are better off using mri_glmfit-sim rather than the command line below. mri_glmfit-sim will run that program giving it the appropriate fwhm.
mri_glmfit --y lh.gender_age.thickness.10.mgh \ --glmdir lh.gender_age.glmdir \ --fsgd gender_age.txt doss \ --surf fsaverage lh \ --fwhm 14.517 --C age.mat \ --sim mc-full 10000 2 lh.gender_age.glmdir/csd1
Do I add the --cache 4 neg \ --overwrite
at the end?
- When I run tksurfer to view the sig.mgh file and I set the
threshold to 2, meaning vertices with p<.01, I have just few vertices coloured in blue. Does this mean a low activation? If yes, what I have to do?
Yes. You can try lowering it to 1.3 (p<.05). If the effect is too subtle, you will need to add more subjects (assuming there is an effect at all). doug
Thank you very much! Antonella
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>
*To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com>> *Cc:* "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
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*Sent:* Wednesday, August 17, 2011 11:53 AM *Subject:* Re: [Freesurfer] mri_glmfit-sim
Antonella Kis wrote:
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?
You would use it in the same place that you would use lh.AGE.thickness.10.mgh. It is just a different way to compute it if you did not qcache.
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?
Yes, use mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite
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?
Run tksurfer to view the sig.mgh file. Set the threshold to the one you used in mri_glmfit-sim using the view->configure->overlay. There are no hard and fast rules to setting thresholds, but people usually use p<.05 or p<.01.
doug
Thank you very much for your valuable help. Antonella
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
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*To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com>
<mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com mailto:atorok9@yahoo.com>>>
*Cc:* "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>>"
<freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
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*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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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html