obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.
Hi,
I would like to to obtain FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a DWI file, either produced by dt_recon (or perhaps better - from Tracula) and an anatomy file in atlas space and then use WMParcStatsLUT.txt or FreeSurferColorLUT.txt (not sure which) to obtain the wm ROIs containing FA data. And then register the aparc+aseg.mgz to the FA image and use mri_segstats to retrieve FA data from the white matter ROIs.
I have done this: # Register DTI file to individual anatomy space 1) dt_recon --i 1/dti/1.dcm --s 001 --b 1/dti/bval 1/dti/bvec --o 1/dtrecon
# Register fa.nii to wmparc.mgz and aparc+aseg.mgz 2) mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 001v4/mri/wmparc.mgz --inv --interp nearest --o 1/mri/aseg2DTI.mgz --no-save-reg mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 001v4/mri/aparc+aseg.mgz --inv --interp nearest --o 1/mri/aparc-aseg2DTI.mgz --no-save-reg
3) It works for wmparc, in that I get data that range from 0.0 to 0.4 with mean = 0.04 (which is a little low for FA values): mri_segstats --seg 1/mri/wmparc2DTI.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i 1/dtrecon/fa.nii --sum fa.stats_wm-lh-medialorbitofrontal
But for aparc+aseg, it doesn't produce any data: mri_segstats --seg 1/mri/aparc-aseg2DTI.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i 1/dtrecon/fa.nii --sum fa.stats_wm-lh-medialorbitofrontal
output: Found 1 segmentations Computing statistics for each segmentation 0 3014 wm-lh-medialorbitofrontal 0 0.000
Reporting on 0 segmentations mri_segstats done
Questions: 1) Am I right to use FreeSurferColorLUT.txt and not WMParcStatsLUT.txt? 2) In order to get FA data from the wm regions corresponding to cortical ROIs, should I use the FA registrated to wmparc.mgz or aparc+aseg.mgz? 3) If I want to use Tracula DTI files instead, which file do I choose: Is it FA_ditifit.nii?
sincerely yours,
Knut Jørgen Bjuland PhD
Hi Knut Jørgen - The aparc+aseg doesn't contain the wm-* labels, only the cortical labels from the aparc (in the 1000's and 2000's) and subcortical labels from the aseg. The wm labels (in the 3000's and 4000's) are in the wmparc only.
a.y ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Knut J Bjuland [knutjorgen@outlook.com] Sent: Wednesday, November 30, 2016 5:35 AM To: Freesurfer support list Subject: [Freesurfer] obtain fa FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt.
Hi,
I would like to to obtain FA data from the white matter ROIs in WMParcStatsLUT.txt. or FreeSurferColorLUT.txt. So would it work to coregister a DWI file, either produced by dt_recon (or perhaps better - from Tracula) and an anatomy file in atlas space and then use WMParcStatsLUT.txt or FreeSurferColorLUT.txt (not sure which) to obtain the wm ROIs containing FA data. And then register the aparc+aseg.mgz to the FA image and use mri_segstats to retrieve FA data from the white matter ROIs.
I have done this: # Register DTI file to individual anatomy space 1) dt_recon --i 1/dti/1.dcm --s 001 --b 1/dti/bval 1/dti/bvec --o 1/dtrecon
# Register fa.nii to wmparc.mgz and aparc+aseg.mgz 2) mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 001v4/mri/wmparc.mgz --inv --interp nearest --o 1/mri/aseg2DTI.mgz --no-save-reg mri_vol2vol --mov 1/dtrecon/fa.nii --reg 1/dtrecon/register.dat --targ 001v4/mri/aparc+aseg.mgz --inv --interp nearest --o 1/mri/aparc-aseg2DTI.mgz --no-save-reg
3) It works for wmparc, in that I get data that range from 0.0 to 0.4 with mean = 0.04 (which is a little low for FA values): mri_segstats --seg 1/mri/wmparc2DTI.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i 1/dtrecon/fa.nii --sum fa.stats_wm-lh-medialorbitofrontal
But for aparc+aseg, it doesn't produce any data: mri_segstats --seg 1/mri/aparc-aseg2DTI.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --id 3014 --i 1/dtrecon/fa.nii --sum fa.stats_wm-lh-medialorbitofrontal
output: Found 1 segmentations Computing statistics for each segmentation 0 3014 wm-lh-medialorbitofrontal 0 0.000
Reporting on 0 segmentations mri_segstats done
Questions: 1) Am I right to use FreeSurferColorLUT.txt and not WMParcStatsLUT.txt? 2) In order to get FA data from the wm regions corresponding to cortical ROIs, should I use the FA registrated to wmparc.mgz or aparc+aseg.mgz? 3) If I want to use Tracula DTI files instead, which file do I choose: Is it FA_ditifit.nii?
sincerely yours,
Knut Jørgen Bjuland PhD
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Knut J Bjuland -
Yendiki, Anastasia