Thank you Doug.

I also just got help from the AFNI message board which solved the problem: so 
here is a note for  AFNI/freesurfer users if they come across this too - if you 
run AFNI's @auto_tlrc command use the  '-rmode NN' so that it does nearest 
neighbor resampling.



----- Original Message -----
From: Doug Greve <[EMAIL PROTECTED]>
Date: Monday, July 28, 2008 1:37 pm
Subject: Re: [Freesurfer] AFNI /freesurfer aseg files problem

> 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 <[EMAIL PROTECTED]>
> >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 <[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
> >>    
> >>
> >>>>>
> >>>>>
> >>>>>_______________________________________________
> >>>>>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
> >>>>[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
> >>>>
> >>>>
> >>>>_______________________________________________
> >>>>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
> >>[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
> >>
> >>
> >>
> >>    
> >>
> >
> >
> >  
> >
> 
> -- 
> 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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