Sorry, don't know anything about those commands. You're probably better off registering the functional data directly to the anatomical (fslregister or spmregister) rather than going thru the talairach transform. You can then use mri_vol2vol to map the functional to the anatomical, then mri_segstats to exctract the average functional value (or you can probably use the afni command at that point).

doug

Liat Levita wrote: 
Hello Doug, 
I transformed the aseg_m file to be 3x3x3.
I will try and trouble shot the possible error in that transform-

The AFNI steps I used to transform the freesurfer files to AFNI format, and than to be 3x3x3 are pasted below.

Liat

-----
foreach subj (xxx)


#step1
@SUMA_Make_Spec_FS -sid ${subj}

#step2

@SUMA_AlignToExperiment \
-exp_anat /Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_anat+orig \
-surf_anat /Volumes/cbgb/Liat/freesurfer_subjects/${subj}/SUMA/${subj}_SurfVol+orig \
-wd \
-prefix ${subj}_AlignExp


#step 3: To align a given parcellation file

3dWarp -NN -matparent ${subj}_AlignExp+orig -prefix ${subj}_aseg_m aseg.nii

#step 4: I transformed the  functional data set by the  talairch transform obtained  for the anatomical data, and then which was resampled to a 3x3x3 space during this step.

@auto_tlrc -apar ${subj}_anat_at+tlrc -input ${subj}_FC_Seed_aseg_fs_AMY_stats_ni_pi_Final+orig -dxyz 3 -suffix _at3

end





----- Original Message -----
From: Doug Greve <greve@nmr.mgh.harvard.edu>
Date: Monday, July 28, 2008 1:07 pm
Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem

  
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
    


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




     

          
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

   

        
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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



    


  

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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