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 On 06/06/2014 02:06 AM, Rotem Saar wrote: > 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 > > > > _______________________________________________ > 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 gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
