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?

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?

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?

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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 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

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.

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.

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 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 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 *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

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:* 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 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Dear Doug,

This is my last question for today and I will be very grateful if you can give me your advise one more time. When I run the: mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite

the threshold is 4 (I am not sure why and if it has to be less for example 1.3 as you suggested) and I get only 3 clusters in my cache.the4. neg.sig.cluster.summary file.

When I load the cluster annotation in tksurfer do I need to set the same threshold?

tksurfer fsaverage lh inflated \ -annot lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot \ -fthresh 2 -curv -gray

I cannot see any colours/clusters on the inflated surface.

If I change in the mri_glmfit-sim the threshold to 1.3 I am getting 5 clusters and still nothing when I load the cluster annotation in tksurfer. I am doing maybe something wrong or i just need more subjects?

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 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 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 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>

...

*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 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>>

...

*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:* 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 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>

...

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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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

---

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Dear Doug,

I know as you told me in past that the average value for the cortical thickness in significant clusters is given in the cache.th20.neg.y.ocn.dat file under lh-Avg-thickness-age-Cor file. 1).Is there another way to get the cortical thickness for the significant clusters, other than read them from the cache.th20.neg.y.ocn.dat file?  Analyzing my results for patients in lh with abnormal  left side (due epilepsy) I realize that my  cortical thickness values in this patients are not different (small difference) from the controls values.

2)Maybe I did  a mistake while setting the FSGD (Y.fsgd) or what other mistake I could do because the cortical thickness should be different in this patients versus controls?

I attached my FSGD matrix as well as my cortical thickness values in the significant clusters.

Thank you very much for your time and help. AK

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 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 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 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 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>

...

*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 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>>

...

*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:* 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 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>

...

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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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

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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 To: Antonella Kis atorok9@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 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

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:* 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 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 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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 *To:* Antonella Kis atorok9@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 <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 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>>

...

*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:* 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 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>

...

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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

...

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

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*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

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...

...

...

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