Hi Doug,
Can be the reason that while getting 5 clusters and loading the annotation in
tksurfer shows me nothing because I got the following error?
Could not read annot file
lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot
No such file or directory
ERROR: could not load
lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot
How can I fix this error?
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 2:55 PM
Subject: Re: [Freesurfer] mri_glmfit-sim
for the cache, the simulation has already been done (using 10,000). This
makes it much faster:).
doug
Antonella Kis wrote:
> 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
> <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:* 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>
> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>>
> > > *To:* Antonella Kis <ator...@yahoo.com <mailto:ator...@yahoo.com>
> <mailto:ator...@yahoo.com <mailto:ator...@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:* 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>>>
> > > > 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>>
> > <mailto: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>
> <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
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
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> <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>
> 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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