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?

2) Are then the mentioned steps the right one to be followed?

3) I saw on one tutorial about the mri_glm to perform estimations. What are this estimations? Do I need to run:

# 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?

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?

5) 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?


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: 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>
> *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:
> >
> > 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
> >
> > 
> ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
> The information in this e-mail is intended only for the person to whom
> it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> but does not contain patient information, please contact the sender
> and properly
> dispose of the e-mail.
>
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer