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
>
>
>
>
>
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