I thought it had to be there because when I don't copy it into the glmdir I get an error message that it can't find the mgh in said glmdir. I'm gonna try running it with the flag you mentioned. What does it mean, though, that it won't compute means over the clusters?

----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 26. Mai 2016 17:15:41 Betreff: Re: [Freesurfer] glmdir question

What is it doing in your glmdir? Usually you'd have it in another location when running mri_glmfit (which creates the glmdir). In any case, you can run it with --no-y and it will not look for the input file (and will not compute means over the clusters).

On 5/26/16 8:56 AM, Clara Kühn wrote:

Dear FreeSurfer Experts,

when running the Monte Carlo correction on a GLM I specify this command: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces

This assumes that my mgh file that I used as input for the GLM is in lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and create a new folder for this GLM I have to copy the mgh file into the glmdir to run the Monte Carlo correction. Is there a way to specify where that mgh is located so that I don't have a bunch of copies of it in all my glmdirs?

Thanks for your help! Cheers Clara

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

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,

I ran this command with the --no-y Flag:

mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 --2spaces --no-y

and got the following error message:

ERROR: Flag --no-y unrecognized. --glmdir /scr/etsch2/kids/ct/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir --cache-dir /scr/etsch2/kids/ct/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 --2spaces --no-y

Does the flag need to be at a certain position? Thanks for your help Clara

----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 26. Mai 2016 17:53:47 Betreff: Re: [Freesurfer] glmdir question

By default it will compute a table. The rows of the table are each subject. The columns are the clusters. Each cell is the mean of the input for that subject over that cluster. It needs the input data to do this.

On 05/26/2016 11:18 AM, Clara Kühn wrote:

I thought it had to be there because when I don't copy it into the glmdir I get an error message that it can't find the mgh in said glmdir. I'm gonna try running it with the flag you mentioned. What does it mean, though, that it won't compute means over the clusters?

----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 26. Mai 2016 17:15:41 Betreff: Re: [Freesurfer] glmdir question

What is it doing in your glmdir? Usually you'd have it in another location when running mri_glmfit (which creates the glmdir). In any case, you can run it with --no-y and it will not look for the input file (and will not compute means over the clusters).

On 5/26/16 8:56 AM, Clara Kühn wrote:

...

Dear FreeSurfer Experts,

when running the Monte Carlo correction on a GLM I specify this command: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces

This assumes that my mgh file that I used as input for the GLM is in lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and create a new folder for this GLM I have to copy the mgh file into the glmdir to run the Monte Carlo correction. Is there a way to specify where that mgh is located so that I don't have a bunch of copies of it in all my glmdirs?

Thanks for your help! Cheers Clara

---

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

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.

---

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

Hm. It either doesn't recognize the --no-y flag (no matter at which position) or it doesn't recognize the --mczsim flag.

----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 26. Mai 2016 18:58:39 Betreff: Re: [Freesurfer] glmdir question

Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim

On 05/26/2016 12:53 PM, Clara Kühn wrote:

Hi Doug,

I ran this command with the --no-y Flag:

mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 --2spaces --no-y

and got the following error message:

ERROR: Flag --no-y unrecognized. --glmdir /scr/etsch2/kids/ct/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir --cache-dir /scr/etsch2/kids/ct/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 --2spaces --no-y

Does the flag need to be at a certain position? Thanks for your help Clara

----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 26. Mai 2016 17:53:47 Betreff: Re: [Freesurfer] glmdir question

By default it will compute a table. The rows of the table are each subject. The columns are the clusters. Each cell is the mean of the input for that subject over that cluster. It needs the input data to do this.

On 05/26/2016 11:18 AM, Clara Kühn wrote:

...

I thought it had to be there because when I don't copy it into the glmdir I get an error message that it can't find the mgh in said glmdir. I'm gonna try running it with the flag you mentioned. What does it mean, though, that it won't compute means over the clusters?

----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Donnerstag, 26. Mai 2016 17:15:41 Betreff: Re: [Freesurfer] glmdir question

What is it doing in your glmdir? Usually you'd have it in another location when running mri_glmfit (which creates the glmdir). In any case, you can run it with --no-y and it will not look for the input file (and will not compute means over the clusters).

On 5/26/16 8:56 AM, Clara Kühn wrote:

...

Dear FreeSurfer Experts,

when running the Monte Carlo correction on a GLM I specify this command: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces

This assumes that my mgh file that I used as input for the GLM is in lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and create a new folder for this GLM I have to copy the mgh file into the glmdir to run the Monte Carlo correction. Is there a way to specify where that mgh is located so that I don't have a bunch of copies of it in all my glmdirs?

Thanks for your help! Cheers Clara

---

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

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.

---

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

Dear FreeSurfer experts,

I would like to correlate my thickness data with behavioral measures. Can I do that with glmfit? If so, could you explain how to specify the contrast for that? My fsgd file looks like this:

GroupDescriptorFile 1 Class 1male plus blue Class 1female plus red Class 2male circle blue Class 2female circle red Class 3male triangle blue Class 3female triangle red Variables age_sc1 Mottier Input subject1 1female 51.61 10 Input subject2 1female 48.89 15 ...

Thank you! Clara

I have and it's been very helpful. I'm not sure though where a correlation was specified in those examples. If I understand it correctly, I have to set my groups to 0 and my covariate to 1. The columns in my designamtrix look like this:

1male 1female 2male 2female 3male 3female 1male_behavior 1female_behavior 2male_behavior 2female_behavior 3male_behavior 3female_behavior

So if I want to test the correlation between thickness and behavior across all groups the contrast would be this: 0 0 0 0 0 0 1 1 1 1 1 1 or would it have to be 1/3 instead of 1 because I have 3 groups? Or even 1/6 because of my 3 groups with 2 levels each?

Thanks Clara

----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 31. Mai 2016 19:18:40 Betreff: Re: [Freesurfer] correlation with glm

have you seen our worked-out examples?

http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

On 05/31/2016 03:39 AM, Clara Kühn wrote:

Dear FreeSurfer experts,

I would like to correlate my thickness data with behavioral measures. Can I do that with glmfit? If so, could you explain how to specify the contrast for that? My fsgd file looks like this:

GroupDescriptorFile 1 Class 1male plus blue Class 1female plus red Class 2male circle blue Class 2female circle red Class 3male triangle blue Class 3female triangle red Variables age_sc1 Mottier Input subject1 1female 51.61 10 Input subject2 1female 48.89 15 ...

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