Dear freesurfer experts,

I'm using the attached script to perform diffusion analysis for 3T Philips dicoms, 16 gradients. I want to end with a specific FA value for each segment. During the analysis I noticed an artifact (see attached pic) which I don't really understand. I double-checked my data using DICOM-viewer and some other DTI software and the data seems fine - no artifacts (I but I don't want to use other software, as I already performed volumetric analysis to these subjects using freesurfer and now interested to expand the volumetric results and give both volume+FA values to each segment). Another question I have is regarding the FA values I get - for example, I'm getting CC fa values between 0.45-0.75 - does this make sense ? Shouldn't they be more like 0.6-0.8 ? (subjects are healthy students, age range: 25-30). Can u please look at the script and highlight what I'm doing wrong ? Will you agree to look at my data if I will send a folder with one subject ?

Thanks in advance

Rotem

 

1) dt_recon --i /usr/local/freesurfer/subjects/Anatomy1627/DTI/I160.dcm --s Anatomy1627 --o /usr/local/freesurfer/subjects/Anatomy1627/DTI --b /usr/local/freesurfer/subjects/Anatomy1627/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy1627/DTI/bvecs.bvec

To check results, run:

tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy1627/DTI/lowb.nii --reg /usr/local/freesurfer/subjects/Anatomy1627/DTI/register.dat --surf

2) tkmedit Anatomy1627 orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/Anatomy1627/DTI/register.dat -overlay /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa.nii -fthresh 0.2 -fmax 1

3) mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa.nii --targ /usr/local/freesurfer/subjects/Anatomy1627/mri/orig.mgz --s Anatomy1627 --interp nearest --o /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.nii --reg /usr/local/freesurfer/subjects/Anatomy1627/DTI/register.dat

To check results, run:

tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.nii --targ /usr/local/freesurfer/subjects/Anatomy1627/mri/orig.mgz --reg /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.nii.reg

4) mri_mask /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.nii /usr/local/freesurfer/subjects/Anatomy1627/mri/brainmask.mgz /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.mask.nii

To check results, run:

 

tkmedit Anatomy1627 /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.mask.nii

5) mri_segstats --seg /usr/local/freesurfer/subjects/Anatomy1627/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy1627/DTI/fa_Anatomy1627.mask.nii --sum /usr/local/freesurfer/subjects/Anatomy1627/stats/all_stats_fa_Anatomy1627