aparc2aseg using Destrieux atlas now seems to run OK for a different subject anyway - and I managed to get the same image as you did. But there are two problems: 1. when I do tkmedit subjid T1.mgz -segmentation wmparc.a2009s.mgz with color LUT, it still shows Killiany/Desikan conventions for wm parcels. Why is this?
2. despite the above trouble I ran mri_segstats --seg MPRAGE07/mri/wmparc.a2009s.mgz --sum MPRAGE07/stats/wmparc.a2009s.stats --pv MPRAGE07/mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask MPRAGE07/mri/brainmask.mgz --in MPRAGE07/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject MPRAGE07 --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
(MPRAGE07 is my subjid) - it ended prematurely declaring
atlas_icv (eTIV) = 1299492 mm^3 (det: 1.499128 ) Loading MPRAGE07/mri/wmparc.a2009s.mgz Getting Cerebral WM volumes from surface lh white matter volume 210579 rh white matter volume 206282 Loading MPRAGE07/mri/norm.mgz Loading MPRAGE07/mri/norm.mgz Loading MPRAGE07/mri/brainmask.mgz # nbrainmaskvoxels 1469167 # brainmaskvolume 1469167.0 # nbrainsegvoxels 252233 # brainsegvolume 252233.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1190 segmentations Computing statistics for each segmentation 1 1 Left-Cerebral-Exterior 0 2 2 Left-Cerebral-White-Matter Segmentation fault Why is this?
Many thanks Lena
On 16/02/2010 19:27, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
which version of freesurfer is being used? (although i dont think it should matter).
is the talairach.xfm correct?
attached is a snapshot of running what i suggested on a subject of my own, and it appears correct.
i am using this to display:
tkmedit subjid T1.mgz -segmentation wmparc.mgz
which uses the default color table.
n.
On Tue, 2010-02-16 at 18:21 +0000, Lena Palaniyappan wrote:
Dear Nick
This is exactly what I have been doing for last 3 days!!! - took the last 2 commands and made changes as you suggested. But the resultant wmparc.a2009s.mgz is bizarre - showing lots of out of bounds regions and pointing parahippocampus somewhere near frontal cortex (when using LUT to view the segmentation) - see attached
Is this a problem with LookupTable? I am not sure if I will get the statistics if I move on to segstats with this issue (I was about to giveup when this reply came in-- THANKS!)
Lena
On 16/02/2010 17:33, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
To get the Destrieux atlas parcellations in the wmparc, first have a look at the -wmparc section of the recon-all table:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
those last two commands would be modified like this:
mri_aparc2aseg --s <subjid> --labelwm --hypo-as-wm --rip-unknown --ribbon --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz
mri_segstats --seg mri/wmparc.a2009s.mgz --sum stats/wmparc.a2009s.stats ... (all those other args)
the important change was to mri_aparc2aseg, where i change the --ctxseg arg to aparc.a2009s+aseg.mgz, as that is the Destrieux atlas. the other change was just changing the 'wmparc' name to 'wmparc.a2009s', just to be consistent with naming.
probably we should modify recon-all so that wmparc.a2009s.stats is created by default.
you could also 'cheat' by just copying aparc.a2009s+aseg.mgz overtop aparc+aseg.mgz and then running 'recon-all -s subj -wmparc', but that can make keeping track of what's what more difficult.
n.
On Mon, 2010-02-15 at 15:19 +0000, Lena Palaniyappan wrote:
Hi all
Could anyone help me with extracting the wmparc volume stats in accordance with Destrieux atlas?
As it stands now the segmentations corresponding to whitematter beneath Destrieux 2009 parcellations are returned empty when called for
Many thanks Lena
_________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
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Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH
_______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH