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
>
>
>
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