I too am puzzled as to why you would want to do this. In terms of getting improvement in the alignment across subjects TBSS is one way to approach this. Another would be to use the fiber orientations in the registration like these folks have done: http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage

If you are interested in studying the properties of cortical grey matter there might be better modalities than FA. If you can provide more details on what you are trying to do, perhaps that would clarify how to go about it?

Peace,

Matt.

On 3/22/16, 2:49 PM, "Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:

I don't know of a reference where someone has done this (though I would be surprised if it is not out there), so just be aware of this if you try to publish. The commands look correct, however, you may or may not want to sample in the middle of the cortical ribbon (--projfrac 0.5). Since this is a DTI analysis, wouldn't you want to sample in the WM? Doing that is a little tricky, but you can use something like --projabs -1 to sample 1mm *away* from the ribbon into the WM.

On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:

...

Dear FS experts,

I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands:

1.I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold --init-fsl --reg reg.dat

2.I concatenated the subject¹s FA maps using the command : mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out lh.FA.mgz

3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.FA.mgz --tval lh.FA_5mm.mgz

4.Then GLM analysis using mri_glmfit

5.Correction for multiple comparison mri_glmfit-sim

Kindly, are these steps correct? I used the previous steps to do surface based analysis using PET images and it worked very well. While for the FA maps it seems that there is something wrong and I can¹t figure out what it is!

I highly appreciate any input on this!

Best,

Mohamad

---

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Right but what do you think FA, MD, AD, RD, etc are telling you neurobiologically in the grey matter?

Matt.

On 3/23/16, 7:18 PM, "Alshikho, Mohamad J." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of MALSHIKHO@mgh.harvard.edu> wrote:

Hi Matt, I highly appreciate your input on this!!

Actually my goal is to study the difference in FA values between groups within the cortex. I know that diffusivities ( MD, AD and RD) can be used to evaluate gray matter and many people claim that it is much better to use diffusivities to evaluate gray matter But my interest is specifically in FA within the gray matter.

For that reason I want to do surface based analysis to study the differences in FA between my study groups. I checked for the optimal ways to do it:

1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
2. And I found

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028109 .html

I ran the analysis using both methods.

For the second method I replaced PET maps by FA maps and this was the reason for my question! If we can do the analysis that way using PET maps, why we can't do it using FA maps?

I will be more than happy if you can suggest me an alternative approach to study FA on a surface.

Best, Mohamad

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Wednesday, March 23, 2016 8:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface based analysis using FA maps

I too am puzzled as to why you would want to do this. In terms of getting improvement in the alignment across subjects TBSS is one way to approach this. Another would be to use the fiber orientations in the registration like these folks have done: http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage

If you are interested in studying the properties of cortical grey matter there might be better modalities than FA. If you can provide more details on what you are trying to do, perhaps that would clarify how to go about it?

Peace,

Matt.

On 3/22/16, 2:49 PM, "Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:

...

I don't know of a reference where someone has done this (though I would be surprised if it is not out there), so just be aware of this if you try to publish. The commands look correct, however, you may or may not want to sample in the middle of the cortical ribbon (--projfrac 0.5). Since this is a DTI analysis, wouldn't you want to sample in the WM? Doing that is a little tricky, but you can use something like --projabs -1 to sample 1mm *away* from the ribbon into the WM.

On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:

...

Dear FS experts,

I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands:

1.I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold --init-fsl --reg reg.dat

2.I concatenated the subject¹s FA maps using the command : mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out lh.FA.mgz

3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.FA.mgz --tval lh.FA_5mm.mgz

4.Then GLM analysis using mri_glmfit

5.Correction for multiple comparison mri_glmfit-sim

Kindly, are these steps correct? I used the previous steps to do surface based analysis using PET images and it worked very well. While for the FA maps it seems that there is something wrong and I can¹t figure out what it is!

I highly appreciate any input on this!

Best,

Mohamad

---

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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FA or fractional anisotropy explains the fraction of the diffusion that is along the long axis of the diffusion tensor. In so far as the diffusion tensor is an accurate model of the underlying structural architecture, what you say might be true (e.g. in the small number of white matter regions with only one main fiber orientation). Most of white matter has multiple fiber orientations and thus the diffusion tensor is not a great model. In grey matter, the principle orientation of processes is radial to the surface (e.g. radial fibers, major dendrites), but there are are also tangential processes (e.g. Bands of Baillarger). To get a decrease in FA, one could do a number of things:

1) Decrease the strength of radial diffusion 2) Increase the strength of tangential diffusion 3) Decrease the strength of both radial and tangential diffusion

Are you looking for a measure that shows tissue damage?

Matt.

On 3/23/16, 7:55 PM, "Alshikho, Mohamad J." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of MALSHIKHO@mgh.harvard.edu> wrote:

It can explain one thing "tissue integrity"

It will tell us neurobiologically exactly what can tell us in tissues other than the brain such as liver, lung, heart, joints, .... etc

Mohamad

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Wednesday, March 23, 2016 8:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface based analysis using FA maps

Right but what do you think FA, MD, AD, RD, etc are telling you neurobiologically in the grey matter?

Matt.

On 3/23/16, 7:18 PM, "Alshikho, Mohamad J." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of MALSHIKHO@mgh.harvard.edu> wrote:

...

Hi Matt, I highly appreciate your input on this!!

Actually my goal is to study the difference in FA values between groups within the cortex. I know that diffusivities ( MD, AD and RD) can be used to evaluate gray matter and many people claim that it is much better to use diffusivities to evaluate gray matter But my interest is specifically in FA within the gray matter.

For that reason I want to do surface based analysis to study the differences in FA between my study groups. I checked for the optimal ways to do it:

1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
2. And I found

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028 109 .html

I ran the analysis using both methods.

For the second method I replaced PET maps by FA maps and this was the reason for my question! If we can do the analysis that way using PET maps, why we can't do it using FA maps?

I will be more than happy if you can suggest me an alternative approach to study FA on a surface.

Best, Mohamad

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Wednesday, March 23, 2016 8:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface based analysis using FA maps

I too am puzzled as to why you would want to do this. In terms of getting improvement in the alignment across subjects TBSS is one way to approach this. Another would be to use the fiber orientations in the registration like these folks have done: http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage

If you are interested in studying the properties of cortical grey matter there might be better modalities than FA. If you can provide more details on what you are trying to do, perhaps that would clarify how to go about it?

Peace,

Matt.

On 3/22/16, 2:49 PM, "Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:

...

I don't know of a reference where someone has done this (though I would be surprised if it is not out there), so just be aware of this if you try to publish. The commands look correct, however, you may or may not want to sample in the middle of the cortical ribbon (--projfrac 0.5). Since this is a DTI analysis, wouldn't you want to sample in the WM? Doing that is a little tricky, but you can use something like --projabs -1 to sample 1mm *away* from the ribbon into the WM.

On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:

...

Dear FS experts,

I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands:

1.I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold --init-fsl --reg reg.dat

2.I concatenated the subject¹s FA maps using the command : mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out lh.FA.mgz

3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.FA.mgz --tval lh.FA_5mm.mgz

4.Then GLM analysis using mri_glmfit

5.Correction for multiple comparison mri_glmfit-sim

Kindly, are these steps correct? I used the previous steps to do surface based analysis using PET images and it worked very well. While for the FA maps it seems that there is something wrong and I can¹t figure out what it is!

I highly appreciate any input on this!

Best,

Mohamad

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The point is that more than tissue damage will cause changes to FA.

Matt.

On 3/23/16, 9:17 PM, "Alshikho, Mohamad J." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of MALSHIKHO@mgh.harvard.edu> wrote:

This is theoritically correct! If we do DTI to study the liver. How these measures can explain the tissue? It is not only white matter and gray matter!

All DTI measures can explain how much space we have between the cells. More space means low FA and high RD. The opposit correct as well. Given that they share the same formula. If we accept RD as a marker for gray matter integrity. We should accept FA a marker for gray matter integrity.

Yes I am looking for an optimal measure to evaluate tissue damage.

Mohamad ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Matt Glasser [matt@ma-tea.com] Sent: Wednesday, March 23, 2016 9:29 PM To: Freesurfer support list Subject: Re: [Freesurfer] Surface based analysis using FA maps

FA or fractional anisotropy explains the fraction of the diffusion that is along the long axis of the diffusion tensor. In so far as the diffusion tensor is an accurate model of the underlying structural architecture, what you say might be true (e.g. in the small number of white matter regions with only one main fiber orientation). Most of white matter has multiple fiber orientations and thus the diffusion tensor is not a great model. In grey matter, the principle orientation of processes is radial to the surface (e.g. radial fibers, major dendrites), but there are are also tangential processes (e.g. Bands of Baillarger). To get a decrease in FA, one could do a number of things:

1. Decrease the strength of radial diffusion
2. Increase the strength of tangential diffusion
3. Decrease the strength of both radial and tangential diffusion

Are you looking for a measure that shows tissue damage?

Matt.

On 3/23/16, 7:55 PM, "Alshikho, Mohamad J." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of MALSHIKHO@mgh.harvard.edu> wrote:

...

It can explain one thing "tissue integrity"

It will tell us neurobiologically exactly what can tell us in tissues other than the brain such as liver, lung, heart, joints, .... etc

Mohamad

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Wednesday, March 23, 2016 8:49 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface based analysis using FA maps

Right but what do you think FA, MD, AD, RD, etc are telling you neurobiologically in the grey matter?

Matt.

On 3/23/16, 7:18 PM, "Alshikho, Mohamad J." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of MALSHIKHO@mgh.harvard.edu> wrote:

...

Hi Matt, I highly appreciate your input on this!!

Actually my goal is to study the difference in FA values between groups within the cortex. I know that diffusivities ( MD, AD and RD) can be used to evaluate gray matter and many people claim that it is much better to use diffusivities to evaluate gray matter But my interest is specifically in FA within the gray matter.

For that reason I want to do surface based analysis to study the differences in FA between my study groups. I checked for the optimal ways to do it:

1. I found https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon
2. And I found

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/028 109 .html

I ran the analysis using both methods.

For the second method I replaced PET maps by FA maps and this was the reason for my question! If we can do the analysis that way using PET maps, why we can't do it using FA maps?

I will be more than happy if you can suggest me an alternative approach to study FA on a surface.

Best, Mohamad

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Matt Glasser Sent: Wednesday, March 23, 2016 8:04 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface based analysis using FA maps

I too am puzzled as to why you would want to do this. In terms of getting improvement in the alignment across subjects TBSS is one way to approach this. Another would be to use the fiber orientations in the registration like these folks have done: http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Main.HomePage

If you are interested in studying the properties of cortical grey matter there might be better modalities than FA. If you can provide more details on what you are trying to do, perhaps that would clarify how to go about it?

Peace,

Matt.

On 3/22/16, 2:49 PM, "Douglas N Greve" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of greve@nmr.mgh.harvard.edu> wrote:

...

I don't know of a reference where someone has done this (though I would be surprised if it is not out there), so just be aware of this if you try to publish. The commands look correct, however, you may or may not want to sample in the middle of the cortical ribbon (--projfrac 0.5). Since this is a DTI analysis, wouldn't you want to sample in the WM? Doing that is a little tricky, but you can use something like --projabs -1 to sample 1mm *away* from the ribbon into the WM.

On 03/22/2016 11:08 AM, Alshikho, Mohamad J. wrote:

...

Dear FS experts,

I would like to run surface based analysis using FA maps. I am not exactly sure that what I am doing is totally right specially step 2 . I used the following commands:

1.I registered the FA maps to T1 using the command: bbregister --s bert --mov dtifit_FA.nii --bold --init-fsl --reg reg.dat

2.I concatenated the subject¹s FA maps using the command : mris_preproc ­target fsaverage ­hemi lh ­iv .bert1/dtifit_FA.nii reg.dat ­iv bert2/dtifit_FA.nii reg.dat Š. --projfrac 0.5 --out lh.FA.mgz

3.Then smoothing mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval lh.FA.mgz --tval lh.FA_5mm.mgz

4.Then GLM analysis using mri_glmfit

5.Correction for multiple comparison mri_glmfit-sim

Kindly, are these steps correct? I used the previous steps to do surface based analysis using PET images and it worked very well. While for the FA maps it seems that there is something wrong and I can¹t figure out what it is!

I highly appreciate any input on this!

Best,

Mohamad

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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