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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Liat Levita