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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" <ayend...@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" <swinkel...@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 --> 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: swinkel...@northwell.edu<mailto:swinkel...@northwell.edu>
Northwell Health
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