I would suspect that something happened when you converted to afni format. The aseg starts out at 1mm3, 256^3, but it appears to be 3mm3, 54x64x50. These conversions are quit tricky and easy to get wrong. Also, did you check the aseg.stats file to assure that the volumes of the amyg are more-or-less symetrical?
doug
R-to-L extent: -79.500 [R] -to- 79.500 [L] -step- 3.000 mm [ 54 voxels] A-to-P extent: -79.500 [A] -to- 109.500 [P] -step- 3.000 mm [ 64 voxels] I-to-S extent: -63.500 [I] -to- 83.500 [S] -step- 3.000 mm [ 50 voxels]
Liat Levita wrote:
Hi Doug, I just checked, yes they are.
Liat
PS. I attached the Info files to this message.
----- Original Message ----- From: Doug Greve greve@nmr.mgh.harvard.edu Date: Monday, July 28, 2008 12:16 pm Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem
are you sure that t1rc and pscA are the same dimension? Remember, freesurfer resamples everything into 1mm3, 256^3
doug
Liat Levita wrote:
Hello, I wonder if anyone using AFNI converted freesurfer files has come
across this problem (or can tell me if I making an error somewhere that I am just not seeing right now). I posted the same question on the AFNI board but haven't gotten feedback as yet.
Here is the problem:
After using freesurfer to get subcortical segmentations, I
converted the resulting freesurfer files to AFNI format, which was fine - I had no problems doing that. However, when I try use these subcortical segmentation data files (subjectID_aseg_m_at3+tlrc) as masks to pull put PSC signal from each region of interest, I am getting an odd effect of right versus left; whereby left clusters output is fine ( voxel numbers are correct after 3dmaskave), but for the left it is very wrong. I have checked that the labels of the ROIs I am using are correct on AFNI GUI and they are. (code and output below)
I am a bit at a loss; any help will be much appreciated.
Liat
AFNI Code used
Foreach subj (xxx) foreach cluster (18 54) 3dmaskave -q -mask ${subj}_aseg_m_at3+tlrc -mrange ${cluster}
${cluster} \
"${subj}_all_runs_pscA_at3+tlrc" >
${subj}_fsROI_PSC_cluster_${cluster}.1D
end end
Output (get the same odd voxel output from all right hand side of
the brain freesurfer generated ROIs)
*For cluster 18 Left Amygdala ++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] +++ 37 voxels survive the mask
*For cluster 54 Right Amygdala ++ 3dmaskave: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] +++ 200 voxels survive the mask
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