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
>
Info_pscA_at3+tlrc
Description: Binary data
info_aseg_m_at+tlrc
Description: Binary data
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
