Hi Doug,
Thank you very much for your answers!

Kindly I have one more question:
At the end of DTI analysis using the tool “dt_recon” we will have  “ stats” file including the FA value for every segment and parcellate in the brain. Depending on this output can we use the term “ DTI morphometry” to describe the analysis?

Thanks
Mohamad

From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Monday, September 28, 2015 11:26 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] dt_recon

On 9/25/15 9:28 AM, Alshikho, Mohamad J. wrote:
Hi Doug and Bruce,
After running the command :
dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti                  <<< source:   Freesurfer wiki>>>

I need to generate the final statistics ( FA for every parcellate and segment in aseg and wmparc atlases) using the command “mri_segstats”

In order to do so I need to move “fa.nii” to anatomical space using the command:

mri_vol2vol –mov fa.nii –lta register.lta –fstarg –o fa.anat.mgh                  <<< source:   Freesurfer wiki>>>

My questions are about the file “register.lta” :

1.       What is the difference between this file and the file “register.dat” ( which I can see it as an output of  the command ” bbregister” in the final analysis using the command “dt_recon”)
They hold the same basic registration information just in different formats. We are trying to move to the LTA as it is a much better format for these things.

2.       How can I generate the file “ register.lta”?
Use lta_convert, something like
   lta_convert --inreg register.dat --outlta register.lta --src lowb.nii.gz --trg $SUBJECTS_DIR/$subject/mri/orig.mgz

3.       Can I feed the file “ register.dat” instead of the file “ register.lta” into the command “mri_vol2vol “  (in order to move the ‘’fa.nii” to anatomical space). If so which flag I should use instead of the flag “--lta” in the command mri_vol2vol?
Yes, pass it with --reg flag.

Many thanks
Mohamad

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