Dear Allison,

Thank you very much for your email.

1). I wonder if the GLM group analysis that is described on the webpage you sent me (as instructed by Doug and Bruce, I was aware of this webpage and I used it for my QDEC studies but I am not sure if can be used for DTI data analysis) can be used for a DTI group analysis.

Can I use the tksurfer to analyse  my data and see the significant clusters OR I will need to use the freeview as described on the DTI basic website?

2). Also registration of lowb to same-subject anatomical using FSLs flirt creates mask.nii and register.dat files. Can you please expalin what is the mask.nii?

3). Is fa-tal.nii the resampled image in TAL_to_avg35 template?

4) How can I gaet the TAL_to_avg35 template?

Thank you very much for your time and valuable help.

Best regards, Antonella

________________________________ From: Allison Player astevens@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, November 30, 2011 5:11 PM Subject: Re: [Freesurfer] resampled image of the diffusion data to structural data

Antonella, Please refer to this website for help with group analysis: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

On Wed, 30 Nov 2011, Antonella Kis wrote:

Dear FS experts,

1. From dt_recon --help I found that:

Registration of lowb to same-subject anatomical using FSLs flirt creates mask.nii and register.dat

I would appreciate if you can let me know  if mask.nii is the resampled image of any of my diffusion related files in the structural space. If not what is the name of this resampled image after I ran dt_recon? Do I need to have the resampled image of my diffusion data to the structural space before I run the GLM group analysis in TAL space?

2. How can I get the TAL_to_avg35 template?

3. How can I analyze my GLM group analysis, or how can I find if there are

clusters that survived after multiple comparison. What I see on the dt_recon webpage is:

mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean mri_binarize --i group-masksum-tal.nii --min .999 --o group-mask-tal.nii

mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd your.fsgd --C contrast --glmdir groupanadir

What is the meaning of the 0.99n value? Can you please advise me how to do my data analysis for this GLM group study of my DTI data?

THANK YOU!

Antonella

_______________________________________________

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.