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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 à  aparc.a2009s+aseg+2mm

2.       TBSS in FSL to obtain à 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.edu

 

Northwell Health

Visit us at Northwell.edu

 


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