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
> > >
> > > 2) Are then the mentioned steps the right
one to be followed?
> > yes
> > >
> > > 3) 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?
> > >
> > > 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?
> > 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>
> > <mailto:
freesurfer@nmr.mgh.harvard.edu <mailto:
freesurfer@nmr.mgh.harvard.edu>>"
> > <
freesurfer@nmr.mgh.harvard.edu <mailto:
freesurfer@nmr.mgh.harvard.edu> <mailto:
freesurfer@nmr.mgh.harvard.edu <mailto:
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 <mailto:
greve@nmr.mgh.harvard.edu>
> > <mailto:
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu>>
> > > <mailto:
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>>
> > <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>
> > <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>>>>
> > > > *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>
> > <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 <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>>>>
> > > > >
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> <mailto:
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu>>
> > <mailto:
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu> <mailto:
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu>>>
> > > <mailto:
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu> <mailto:
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu>>
> > <mailto:
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu> <mailto:
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 <mailto:
greve@nmr.mgh.harvard.edu> <mailto:
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu>>
> > <mailto:
greve@nmr.mgh.harvard.edu <mailto:
greve@nmr.mgh.harvard.edu> <mailto:
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
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
> > >
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Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:
Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu>>
> > <mailto:
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Freesurfer@nmr.mgh.harvard.edu>
> > <mailto:
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> <mailto:
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
> >
> > _______________________________________________
> > Freesurfer mailing list
> >
Freesurfer@nmr.mgh.harvard.edu <mailto:
Freesurfer@nmr.mgh.harvard.edu> <mailto:
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
>
> _______________________________________________
> Freesurfer mailing list
>
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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.eduPhone 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