Dear Lilla,

Thank you very much for your directions. Sorry I have so many questions but I am  new to this type of research.

I will appreciated a lot if you confirm my understanding regarding some outputs from dtrecon:

1) Is the mask.nii a mask, a binary image of the anatomical to diffusion image of the same subject?

2) Is the mask-tal.nii a mask, a binary image of the  diffusion image to TAL space of one subject?

3) Is the fa-tal.nii.reg the transformation from diffusion space to TAL while register.dat is the transformation from diffusion space to anatomical space?

4) If I want to check my DTI data's registration on the anatomical structure for one of my subjects I need first to get the re-sampled image of the DTI registration data so is correct if I run:

mri_vol2vol   --mov /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti.nii.gz \
              --targ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51.nii.gz \
              --reg /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti/register.dat --no-save-reg \
              --o /media/1Tra/Antonella_2011/DTI_FS/dtrecon/C51_dti/C51_dti-to-C51.nii.gz \
              --interp trilin

such that my resampled registered image for my DTI data to the anatomical image is C51_dti_to C51.nii.gz so in order to check if the registration is good or not I can comapre the original anatomical data C51.nii.gz with the DTI data C51_dti.nii.gz and with my registered and resampled image C51_dti-to-C51.nii.gz?


Thank you very much!
Antonella
From: Lilla Zollei <lzollei@nmr.mgh.harvard.edu>
To: Antonella Kis <atorok9@yahoo.com>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Sent: Tuesday, December 6, 2011 5:01 PM
Subject: Re: [Freesurfer] Diffusion Tutorial and GroupAnalysis.csh

Hi Antonella,

> 1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the following scrip: GroupAnalysis.csh with the following instruction:
>
> # Assemble input for group analysis
> set type = CVS-to-avg35    # alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35'
> Can you please explain what means TAL-to-avg35 if my DTI data (FA) is by default registered on the TAL space and I got the file fa-tal.nii? How I can get the TAL-to-avg35 template? Is this different than the one on which my data was registered by default?

There is probably a typo in the tutorial. It should read
# alternatively could be 'TAL' or 'MNI'

You can replace the mri_cvs_registered files with any other tools output that you want to use for your final comparison.

> 3) Can I load my FA group data registered on TAL: group-fa-tal.nii with tkmedit?

Yes, you shoud and also with Freeview.

Lilla


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