Dear Doug,
Thank you very much! I am ready to start doing my analysis but before I start
you were mentioning that for the simulation 10,000 is a good number. You also
suggested me to run:
mri_glmfit-sim \
--glmdir lh.AGE.glmdir \
--cache 4 neg \
--overwrite
but what is the number of the iteration if I run this part? Do I need to add
this and do I need to mention the threshold in the above coding?
THANKS!
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: 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 <gr...@nmr.mgh.harvard.edu>
> *To:* Antonella Kis <ator...@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 <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>
> > *To:* Antonella Kis <ator...@yahoo.com <mailto:ator...@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:* 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>>
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > -- Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@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
> gr...@nmr.mgh.harvard.edu <mailto:gr...@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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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
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The information in this e-mail is intended only for the person to whom it is
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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
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