Hi Charlotte
have you visually inspected them? I would be more concerned about the # of
voxels in wm which is way too low, but it looks like you eroded the wm
mask, so maybe it's ok. Take a look at the surfaces over the data in
tkmedit and see if it appears accurate in subjects like #8. The WM
intensity won't be exactly 110, and is usually below it due to partial
volume effects.
cheers
Bruce
On Mon, 12 Mar 2012, Charlotte Bernard
wrote:
Dear Freesurfer users,
I run FS on my 670 subjects. All the scans were acquired on a 1.5T Philips
scan.
I noticed that my values in the WM are near 100-110 but not exactly 110. I
think it is a problem! Is it link to the 1.5T? How can I fix it?
I joined my log file of QA tools: could you help me to undertand the output?
wm-anat-snr results:
SNR: Anatomical signal-to-noise ratio in white matter
mWM: Mean white matter intensity value
stdWM: Standard deviation of white matter intensity value
voxWM: Total number of white matter voxels in eroded mask
SubjID SNR mWM stdWM voxWM
1 13,37* 104,18 7,79* 24181 <------
2 14,79* 105,90 7,16* 22148 <------
3 13,57* 104,75 7,72* 37341 <------
4 12,67* 104,18 8,22* 29311 <------
5 14,36* 105,44 7,34* 48083 <------
6 11,40* 103,92 9,11* 47704 <------
7 14,52* 104,71 7,21* 25706 <------
8 9,92 101,42 10,22 40187
9 11,31* 104,28 9,22* 22967 <------
10 11,61* 102,92 8,86* 19850 <------
11 14,78* 105,05 7,11* 26607 <------
12 11,36* 105,33 9,27* 15465 <------
13 11,30* 103,69 9,18* 34685 <------
14 11,73* 105,20 8,97* 40471 <------
15 11,92* 104,04 8,73* 13777 <------
16 9,46 102,04 10,79 30314
17 12,60* 106,40 8,44* 38432 <------
I thought it can help me to quickly identify the subjects who didn't work
for this step. For example, the subject n°8 has a problem?
Thanks,
Charlotte
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