The values look about right in the table. Your pipeline looks ok, thought the last step uses fa_FOLDER-NAME.mask.nii instead of the output of mri_vol2vol (fa_FOLDER-NAME.nii). doug
On 03/17/2013 02:16 AM, Rotem Saar wrote: > > Hi all, > I run into somthing that seems odd to me and wanted to consult - > I run the following script for getting the FA values from my DTI > scans: > > 1) dt_recon --i > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s > FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec > 2) tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg > --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii > 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz > -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii > -fthresh 0.2 -fmax 1 > 4) mri_vol2vol --mov > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s > FOLDER-NAME --interp nearest --o > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat > 5) tkregister2 --mov > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii > --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz > --reg > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg > 6) mri_segstats --seg > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii > --sum > /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME > > > I got a table with all the FA values (see attached), for each > segment, but I suspect a problem: I think that the values are too > high (I set the threshold to 0.2-1), am I right ? > Can u guide me regarding what I can do to solve the problem ? in > addition I attached a figure of the corpus-callosum, in which I'm > interested - i't seems that the green area in not big enough, is > this fixable ? > > Thanks ! > > Rotem > > > > _______________________________________________ > 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: 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.
