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