[Freesurfer] extracting FA from FA_skeletonised with freesurfer parcellation

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Hi,

I try to extract FA values from the FSL FA skeleton using the freesurfer aparc.a2009s+aseg+2mm parcellations.

I did the following:

1. Recon-all to obtain --> aparc.a2009s+aseg+2mm

2. TBSS in FSL to obtain --> all_FA_skeletonised

3. Tbss_deproject to split up all_FA_skeletonised into individual skeletons (native space) (*_FA_FA_all_FA_skeletonised.nii.gz)

4. Non-linear transformation of aparc.a2009s+aseg+2mm to subjects' native space (parc2dwi.nii.gz)

5. Creating binary mask for each subjects FA skeleton to exclude 0 voxels (*_FA_skeleton_mask.nii.gz)

6. Extracting FA values using mri_segstats with the following command:

cd subj1/ mri_segstats \ --seg mri/parc2dwi.nii.gz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i skeletons/SPN01_CMH_0001_01_FA_FA_all_FA_skeletonised.nii.gz \ --mask skeletons/SPN01_CMH_0001_01_FA_skeleton_mask.nii.gz \ --excludeid 0 \ --sum skeletons_FA.stats

The FA values I obtain are around 0.1 which is highly unlikely, especially for regions such as the corpus callosum. Is there some obvious error in my approach? Or can someone recommend a different approach? I would be very grateful for some help!

Thanks, Steph

Stephanie Winkelbeiner, MSc Research Coordinator Psychiatry Research Zucker Hillside Hospital 75-59 263 Street Glen Oaks, NY 11004 Tel: (718) 470-4588 Email: swinkelbei@northwell.edumailto:swinkelbei@northwell.edu

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