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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I don't think I would use "DTI Morphometry" to describe it. I'm not sure what term I would use. It is basically a FA ROI analysis
On 10/2/15 1:28 PM, Alshikho, Mohamad J. wrote:
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” :
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.
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
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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Douglas Greve