Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

2016-03-25 Thread Kirstie Whitaker 
I think eroding the region makes sense in general - you just have to be careful 
to exclude subjects who end up with no data (as you discovered!)

You could also look into why these three subjects had such small wm regions 
under entorhinal cortex. My (still) suspicious mind wonders if there is a bad 
reconstruction that is cutting out part of the inferior temporal lobe and 
therefore "squeezing" all of the cortical labels into a smaller volume. This 
would in turn give very small wm volumes.

On the other hand, entorhinal cortex may just have a relatively small amount of 
white matter underlying it because it's so "narrow" such that when you erode by 
1mm you are left with nothing for these three subjects.

Glad you figured out the odd correlations!

Kx

Sent from my iPhone, please excuse any typos or excessive brevity

> On 25 Mar 2016, at 01:22, Elijah Mak  wrote:
> 
> Hi Kirstie,
> 
> Yes indeed there were 3 subjects at the bottom-left of the plot. 
> 
> To account for PV, I eroded the boundaries using -seg-erode 1 during the 
> mri_segstats stage, and this resulted in a few subjects with no data for the 
> WM entorhinal region (although these were saved as "0" in the .stats file). 
> Do people generally do this for DTI studies?
> 
> All good now. 
> 
> Many thanks again, Kirstie.
> 
> Best Wishes,
> Elijah
> 
> 
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

2016-03-24 Thread Anastasia Yendiki 


Hi Elijah - I suggest looking at the axial diffusivity (AD) and radial 
diffusivity (RD) to help you interpret these results. These are the 
diffusivity parallel and perpendicular to the main budnle going through a 
voxel, respectively. Essentially, FA tells you how different the AD and RD 
are from each other, and MD tells you how big AD and RD are in aggregate.


Here are just a couple of all the possible scenarios that can lead to 
opposite FA/MD relationships:


AD increases, RD stays the same => MD increases, FA increases
AD stays the same, RD increases => MD increases, FA decreases

Hope this helps,

a.y

On Thu, 24 Mar 2016, Elijah Mak wrote:


Hi Freesurfer Community,
I recently used mri_segstats to extract FA and MD as suggested
here: http://freesurfer.net/fswiki/FsTutorial/Diffusion

Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at
some of the correlations between FA and MD in the same regions, and came
across a few interesting ones.

wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001
ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020

wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001 

As I understand, a clear-cut interpretation especially with regards to FA
changes is not so easy!  But could someone discuss / speculate as to why FA
and MD could be positively correlated within the entorhinal WM region? That
was found separately within a group of a elderly healthy controls and a
group of dementia subjects.

Thank you for your time!

Best Wishes,
Elijah


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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

2016-03-24 Thread Elijah Mak 
Hi Kirstie,

Yes indeed there were 3 subjects at the bottom-left of the plot.

To account for PV, I eroded the boundaries using *-seg-erode 1* during the
*mri_segstats* stage, and this resulted in a few subjects with no data for
the WM entorhinal region (although these were saved as "0" in the .stats
file). Do people generally do this for DTI studies?

All good now.

Many thanks again, Kirstie.

Best Wishes,
Elijah
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

2016-03-24 Thread Kirstie Whitaker 
Hi Elijah,

Is there any chance you could attach a scatter plot? My suspicious mind thinks 
either a) there are outliers who are doing odd things, or b) the FA values are 
very different to those in other regions and therefore the correlation with MD 
wouldn't be expected to be the same. 

Kx

Sent from my iPhone, please excuse any typos or excessive brevity

> On 24 Mar 2016, at 23:59, Elijah Mak  wrote:
> 
> Hi Alshikho,
> 
> Yes, I am sure :) Same sequence for everyone. 
> 
> Just to add. FA and MD were significantly negatively correlated for the other 
> regions including the fusiform, precuneus, hippocampus, thalamus, etc. 
> 
> So I am very curious about what could be going on with the ERC here?
> 
> Best Wishes,
> Elijah
> 
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> at
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

2016-03-24 Thread Elijah Mak 
Hi Alshikho

,

Yes, I am sure :) Same sequence for everyone.

Just to add. FA and MD were significantly negatively correlated for the
other regions including the fusiform, precuneus, hippocampus, thalamus,
etc.

So I am very curious about what could be going on with the ERC here?

Best Wishes,
Elijah
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

2016-03-24 Thread Alshikho, Mohamad J. 

Are you sure that all your DTI images have the same acquisition parameters?!!






From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Elijah Mak 
[fk...@medschl.cam.ac.uk]
Sent: Thursday, March 24, 2016 7:33 PM
To: Freesurfer support list
Subject: [Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Freesurfer Community,

I recently used mri_segstats to extract FA and MD as suggested here: 
http://freesurfer.net/fswiki/FsTutorial/Diffusion

Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at 
some of the correlations between FA and MD in the same regions, and came across 
a few interesting ones.

wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001
ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020

wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001

As I understand, a clear-cut interpretation especially with regards to FA 
changes is not so easy!  But could someone discuss / speculate as to why FA and 
MD could be positively correlated within the entorhinal WM region? That was 
found separately within a group of a elderly healthy controls and a group of 
dementia subjects.

Thank you for your time!

Best Wishes,
Elijah

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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

[Freesurfer] FA and MD *positively* correlated within same regions ?

2016-03-24 Thread Elijah Mak 
Hi Freesurfer Community,

I recently used mri_segstats to extract FA and MD as suggested here:
http://freesurfer.net/fswiki/FsTutorial/Diffusion

Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at
some of the correlations between FA and MD in the same regions, and came
across a few interesting ones.

wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001
ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020

wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001

As I understand, a clear-cut interpretation especially with regards to FA
changes is not so easy!  But could someone discuss / speculate as to why FA
and MD could be positively correlated within the entorhinal WM region? That
was found separately within a group of a elderly healthy controls and a
group of dementia subjects.

Thank you for your time!

Best Wishes,
Elijah
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