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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