Dear Karl,
Has anybody had any success with the midline rois given by the atlas
curvature.buckner40.filled.desikan_killiany that is automatically applied
by autorecon3 under the newest stable release, version 3.0?
Our trouble lies in the regions labeled corpuscallosum and
<anything>cingulate: this
atlas is giving us a corpus callosum that is exactly the ventral
cingulate sulcus, and the 4
cingulate gyrus segments, which is what we are interested in in this
case, incorrectly
exclude their ventral portion.
I presume this has been made to work at mgh, because Rahul Desikan's
paper contains
an illustration that is anatomically correctly labeled for these regions.
We are providing an orig/001.mgz image to the autorecon1 step that is
talairach aligned,
skull stripped, and resampled to 1.0 mm voxels, but otherwise is a
signed 16-bit
T1-weighted MRI scan. We have thousands of them, collected over the
past 15 years.
We are writing a nifti .nii file, and converting it with
mri_convert -it nii -ic 128 128 96 -oc 128 128 96 -iid -1.0 0.0 0.0
/raid1/structural/MR/9517294/0036195/10_ACPC/0036195_10_T1_brain.nii
/raid1/data/methods/atlas/parcel/lobes/cloud_study/clipped_atlas_hand_masks/iowa_cortex_atlas/FreeSurfer_Subjects/IowaFifty_2005_0036195/mri/orig/001.mgz
We actually mean to numerically measure the extent -- the area and
thickness, say -- of
anatomical regions of interest including <anything>cingulate and apply
statistical tests to
these data. A line of guff about Type I and Type II errors and what is
only presumable
when identifying anatomical rois would be of no interest, and considered
needlessly
defensive. After all, the other 29 regions of Desikan's really great
atlas are in working
order!
Do we need to convince Rahul Desikan to release the "correct"
*h.curvature.buckner40.filled.desikan_killiany.gcs files with FreeSurfer 3.0
that correspond to his paper?
Greg Harris
The University of Iowa College of Medicine
Psychiatry NeuroImaging Lab
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