Have you checked if the registered segmentation and the FA map align correctly in freeview?
On Nov 23, 2018 1:27 PM, "Winkelbeiner, Stephanie A" Swinkelbei@northwell.edu wrote:
External Email - Use Caution 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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