You don't want to be averaging zero voxels, so masking makes sense.

When you click on the voxels inside one of those segmentation regions (e.g. one of the CC regions) in freeview, are the FA values that you see high?

On Nov 25, 2018 8:42 AM, "Winkelbeiner, Stephanie A" <Swinkelbei@northwell.edu> wrote:

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Hi Anastasia,

I have checked and they do align. However the freesurfer parcels naturally cover more of the brain than the FA skeletons.
I was wondering if this was the problem?

Therefore I added a binary mask of the FA skeletons.

I also tried subtracting the parcels from the FA skeletons with fslmaths to make sure that only the area of the skeleton is read out. But that doesn't give convincing results either.

Anyone having other suggestions? 

Thanks,
Steph


Sent from my Samsung Galaxy smartphone.

-------- Original message --------
From: "Yendiki, Anastasia" <AYENDIKI@mgh.harvard.edu>
Date: 23/11/18 17:50 (GMT-05:00)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [EXTERNAL] Re: [Freesurfer] extracting FA from FA_skeletonised with freesurfer parcellation

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:

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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