Hi Doug,

You did answered me - but unfortunately I could not use this information to calculate MD maps that I can understand.
Concerning your answers and qs:

1. The b-value I'm using is 800. Even if the MD values depend on my b-value, I still can't understand what those units in freesurfer means...:( is there any place in the web where u elaborate on the calculation ? how does freesurfer calculated the MD values ?

2. I re-checked myself and you are correct, MD values are not constrained to be between 0-1 - but the range of 0-1.5 is the most popular range I see in papers & is the range I get when I use for example vista-soft-master to do fiber-tracking and extract MD values for each fiber. But the thing is I don't want to get an MD value per tract, rather I want a nifti file that will include the MD value for each voxel, the same as I have for the FA maps...  Please have a look in this paper (mean diffusivity graph) - 

http://www.ncbi.nlm.nih.gov/pubmed/?term=Effect+of+head+impacts+on+diffusivity+measures+in+a+cohort+of+collegiate+contact+sport+athletes

They even used freesurfer...do u have any idea how did they get these values ?

3. If we will leave the units issue a side for a moment - do u have any idea how can I create nifti files for each participant with MD values in each voxel ? I have those files for the FA, but I don't know how to extract them for MD (the scripts I'm using for the MD and FA are written below).

Thanks for your help !
_______________________________________________________________________________________________________________________________
Was this ever answered?

1. Units - Not sure what the units of MD are. It might depend on your
b-value
2. MD is not constrained to be between 0 and 1. Where are you getting that?
3. I don't know about the CC values. The CC ROIs are pretty small, and
you might be getting significant partial voluming

doug


---------- Forwarded message ----------
From: Rotem Saar <saar.rotem@gmail.com>
Date: 2014-06-06 9:06 GMT+03:00
Subject: Extracting mean diffusivity values from diffusion data in freesurfer 5.3
To: ‫freesurfer@nmr.mgh.harvard.edu‬


Dear freesurfer experts,

I'm using freesurfer 5.3 for extracting FA and MD values for each region from the *aseg file for each subject.
While I get validated FA values (I validated them with you, the literature and some other software I used), I have a problem getting reasonable MD values.

This is the script I'm using for extracting the MD values:

1) dt_recon --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/I160.dcm --s Anatomy0981 --o /usr/local/freesurfer/subjects/Anatomy0981/DTI --b /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0981/DTI/bvecs.bvec

2) mri_label2vol --seg /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --temp /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --reg /usr/local/freesurfer/subjects/Anatomy0981/DTI/register.dat --o /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz

3) mri_segstats --seg-erode 1 --seg /usr/local/freesurfer/subjects/Anatomy0981/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0981/DTI/forMD.mgz --sum /usr/local/freesurfer/subjects/Anatomy0981/stats/all_stats_MD-masked

It writes *.txt files similar to the ones of the FA (and also the volumetric analysis) which is good, but -

1) I can't understand the units (it is written "unknown"). can u tell me what do these units refer to ?
2) I can't understand why the units I get don't corresponds to the units in the literature (0-1). Is there a transformation I need to apply to these units in order to get the values we all see in the literature (MD values ranges between 0 to 1 in the papers I read).
3) I am concerned about the differences in the values both between and within subjects. For example, see 3 different subjects and their MD values for the corpus-callosum:

subject 1:

 35 251       368      368.0  CC_Posterior                       7.4783     7.9938     0.0000    16.0000    16.0000
 36 252       110      110.0  CC_Mid_Posterior                  56.7273   476.3758     0.0000  5002.0000  5002.0000
 37 253       205      205.0  CC_Central                       992.4537  1806.8883     0.0000  5002.0000  5002.0000
 38 254       132      132.0  CC_Mid_Anterior                 1664.2954  2328.8467    43.0000  5002.0000  4959.0000
 39 255       277      277.0  CC_Anterior                     1723.4620  1914.7883     0.0000  5002.0000  5002.0000

subject 2:

 36 251       328      328.0  CC_Posterior                       0.0000     0.0000     0.0000     0.0000     0.0000
 37 252        78       78.0  CC_Mid_Posterior                  43.9744   226.6371     0.0000  2000.0000  2000.0000
 38 253       100      100.0  CC_Central                       203.0800   779.8602     0.0000  5001.0000  5001.0000
 39 254        83       83.0  CC_Mid_Anterior                  264.5783   364.1581     0.0000  1002.0000  1002.0000
 40 255       321      321.0  CC_Anterior                      985.8879   720.5300     0.0000  3028.0000  3028.0000

subject 3:

 35 251       424      424.0  CC_Posterior                      20.6840     6.6236    10.0000    60.0000    50.0000
 36 252       160      160.0  CC_Mid_Posterior                 143.4312   780.4187     0.0000  5001.0000  5001.0000
 37 253       202      202.0  CC_Central                       538.0248  1143.9441     0.0000  5001.0000  5001.0000
 38 254       179      179.0  CC_Mid_Anterior                  496.5140   623.4088     0.0000  2023.0000  2023.0000
 39 255       361      361.0  CC_Anterior                      211.6094   539.0007     0.0000  2028.0000  2028.0000

the values are really different both within the CC parts of the same subject (does this make any sense ??) and also between subjects...

We ruled out a problem in the gradient matrix (both with you and because the FA values corresponds to reasonable values both from the literature and other software we use).

Can u please advise on how can we solve this issue ? We are in the middle of submission of a very novel study and were required to show addition analysis of the MD values - this is why this is so impotent to us. Attached please find the full *.txt files I got.

Thanks for your help.

Rotem Saar-Ashkenazy

Department of Brain and Cognitive Science
Ben Gurion University of the Negev, Beer-Sheva, 84105

School of Social Work
Ashkelon Academic College, Ashkelon, 78211 

Israel