Good Afternoon,
I am attempting to get a list of cortical
thickness statistics on a group of ROIs. The T2 functional data for the subjects was
previously analyzed in AFNI, where
an ROI mask to be applied to all subjects, was developed. The volume ROI mask was converted
from AFNI BRIK to FreeSurfer .mgz format using mri_convert. Recon-all has been run on all T1 anatomical images and fslregister was
used to register each subject’s anatomical data to the ROI mask. I ran the series of commands below and
got results, but the anatomical locations and Talairaich coordinates from
FreeSurfer are not close to the values I see in AFNI.
How and when should I be aligning the center
and orientation of the average subject with the functional mask from AFNI?
Here
is what I tried, but still did not get accurate results even when mris_info
shows the same for both the anatomy and functional mask image
files:
#
cd
$SUBJECTS_DIR/MSN.0964.anat/mri
mri_convert
--apply_transform transforms/talairach.xfm --conform --devolvexfm MSN.0964.anat
-ic 0 0 0 orig.mgz orig_Talc000.mgz
mri_convert
--like orig_Talc000.mgz --conform --devolvexfm MSN.0964.anat -ic 0 0 0
OR_MASK_0005_clust_400_contiguous+tlrc.mgz
OR_MASK_Talc000.mgz
#
mri_info
orig_Talc000.mgz >mri_info.orig_Talc000.mgz
mri_info
OR_MASK_Talc000.mgz > mri_info.OR_MASK_Talc000.mgz
#
#Using
the group ROI mask as a volume dataset in FreeSurfer, I ran the following
commands:
#
#
Create average subject
cd
$SUBJECTS_DIR
make_average_subject
--out MSNaverage --subjects MSN.0964.anat MSN.0965.anat MSN.0966.anat
MSN.0967.anat MSN.0968.anat MSN.0969.anat MSN.0979.anat MSN.0980.anat
MSN.1001.anat MSN.1003.anat MSN.1039.anat
#
#
Register functional map to average subject.
fslregister
--mov $SUBJECTS_DIR/MSNaverage/mri/OR_MASK_Talc000.mgz --s MSNaverage --reg
$SUBJECTS_DIR/MSNaverage/mri/registerMASK2MSNavg.dat
#
#
Convert functional mask from AFNI to a surface (both volume and surface belong
to the average subject
mri_vol2surf
--src $SUBJECTS_DIR/MSNaverage/mri/OR_MASK_Talc000.mgz --srcreg
$SUBJECTS_DIR/MSNaverage/mri/registerMASK2MSNavg.dat \
--hemi lh --fwhm 6 --out_type mgz --o
$SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-lh.mgz --trgsubject MSNaverage
--nvox $SUBJECTS_DIR/MSNaverage/stats/lh.nvox.dat
mri_vol2surf
--src $SUBJECTS_DIR/MSNaverage/mri/OR_MASK_Talc000.mgz --srcreg
$SUBJECTS_DIR/MSNaverage/mri/registerMASK2MSNavg.dat \
--hemi rh --fwhm 6 --out_type mgz --o
$SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-rh.mgz --trgsubject MSNaverage
--nvox $SUBJECTS_DIR/MSNaverage/stats/rh.nvox.dat
#
#
Map average subject surface to subject MSN.0964.anat
surface
mri_surf2surf
--srcsubject MSNaverage --srcsurfval
$SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-lh.mgz \
--trgsubject MSN.0964.anat --trgsurfval
$SUBJECTS_DIR/MSN.0964.anat/surf/fvol2pialsurf.mgz --hemi
lh
mri_surf2surf
--srcsubject MSNaverage --srcsurfval
$SUBJECTS_DIR/MSNaverage/surf/fvol2pialsurf-rh.mgz \
--trgsubject MSN.0964.anat --trgsurfval
$SUBJECTS_DIR/MSN.0964.anat/surf/fvol2pialsurf.mgz --hemi
rh
#
#Create
a surface cluster & label for each ROI for subject
MSN.0964.anat
#generates
region & fixed mni (mni2tal.mat) coordinates for each
ROI
mri_surfcluster
--in $SUBJECTS_DIR/MSN.0964.anat/surf/lh.fvol2pialsurf.mgz --subject
MSN.0964.anat --hemi lh --annot aparc --thmin 1 --thmax 11 --minarea .01
\
--fixmni --olab lh.pial.surf --sum
$SUBJECTS_DIR/MSN.0964.anat/stats/lh.pial.sum.MSN.0964.anat.txt --o
lh.pial.clustsurf --ocn lh.vertex.pial.ClusterNum
mri_surfcluster
--in $SUBJECTS_DIR/MSN.0964.anat/surf/rh.fvol2pialsurf.mgz --subject
MSN.0964.anat --hemi rh --annot aparc --thmin 1 --thmax 11 --minarea .01
\
--fixmni --olab rh.pial.surf --sum
$SUBJECTS_DIR/MSN.0964.anat/stats/rh.pial.sum.MSN.0964.anat.txt --o
rh.pial.clustsurf --ocn rh.vertex.pial.ClusterNum
#
#
Generate statistics for each ROI for each subject
set
left_rois = ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15
)
set
right_rois = ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 17 18 19 20
)
foreach right_roi ( $right_rois
)
mri_label2label --srcsubject
MSNaverage --srclabel
$SUBJECTS_DIR/MSNaverage/label/rh.pial.surf-00${right_roi}.label --trgsubject
MSN.0964.anat --trglabel
$SUBJECTS_DIR/MSN.0964.anat/label/rh.pial.surf-00${right_roi}.label --regmethod
surface --hemi rh
mris_anatomical_stats -l rh.pial.surf-00${right_roi}.label -f
$SUBJECTS_DIR/MSN.0964.anat/stats/rh.ROI${right_roi}.pial.surfstats -b
MSN.0964.anat rh white
end
foreach left_roi ( $left_rois
)
mri_label2label --srcsubject
MSNaverage --srclabel
$SUBJECTS_DIR/MSNaverage/label/lh.pial.surf-00${right_roi}.label --trgsubject
MSN.0964.anat --trglabel
$SUBJECTS_DIR/MSN.0964.anat/label/lh.pial.surf-00${right_roi}.label --regmethod
surface --hemi lh
mris_anatomical_stats -l
lh.pial.surf-00${left_roi}.label -f
$SUBJECTS_DIR/MSN.0964.anat/stats/lh.ROI${left_roi}.pial.surfstats -b
MSN.0964.anat lh white
end#
Any insight on this process would be
greatly appreciated.
Thanks very much for your help.
Denise M.
Cote
Sr. Research
Assistant
Transdisciplinary Research
Group