Hi Liat-
If you converted directly using mri_convert, you may run into some
problems. If so, I suggest using the program Ziad wrote
(@SUMA_Make_Spec_FS) which takes care of some of the freesurfer/AFNI
conversion problems automatically. See the AFNI posts on this issue.
Anthony
Doug Greve wrote:
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 <[EMAIL PROTECTED]>
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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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--
Anthony Steven Dick, Ph.D.
Post-Doctoral Fellow
Human Neuroscience Laboratory
Department of Neurology
The University of Chicago
5841 S. Maryland Ave. MC-2030
Chicago, IL 60637
Phone: (773)-834-7770
Email: [EMAIL PROTECTED]
Web: http://home.uchicago.edu/~adick/
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