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Thanks for your interest in my problem and your help, Anastasia! I will do that!
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Monday, November 26, 2018 3:51 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation
External Email. Use Caution. In that case, it seems that the low values are introduced when transforming the skeleton from template space to individual space. If this is so, it has nothing to do with using the freesurfer segmentation per se. I would ask on the FSL list.
On Nov 26, 2018 3:41 PM, "Winkelbeiner, Stephanie A" <Swinkelbei@northwell.edumailto:Swinkelbei@northwell.edu> wrote:
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So, I initially did that with the all_FA_skeletonised and got values around 0.6 for the Cc as expected. Interestingly enough though, when I do the same with the individual FA_skeletons that I obtained with the tbss_deproject command the values are around 0.1…
Could you think of a reason why that is?
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Monday, November 26, 2018 1:58 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation
External Email. Use Caution.
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.edumailto: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.edumailto:AYENDIKI@mgh.harvard.edu>
Date: 23/11/18 17:50 (GMT-05:00)
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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 --> 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
Northwell Health
Visit us at Northwell.eduhttp://northwell.edu/
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