This page was created to keep a running list of
notes specific to this dataset. To add notes to this page, just open this
page with Netscape Composer and add your notes. This page was created 10/7/03.
Last modified: 5/4/04
The original data can be found in /data/edevel/YALE
Included on this page:
Naming scheme key
Processing flowchart
Measures and Analysis
Special Notes
NAMING SCHEME
avg_305_AIR1ord-
signifies that the file has been taken to 305 space, 12 parameters
brain-
skull stripped file
csf/greyonly-
mask file for csf or grey respectively
flip-
The file has been flipped so that left is
in left space and right is in right space (in the original files
of this dataset, the scans were acquired opposite to this. This was not
caught and corrected until later in processing)
mask-
binary mask file
new-
most recent/correct version of file, should
be used
old-
older version of file, shouldn't be used unless no
new version of file in directory can be found
reslice-
registered structural mri scan (dimensions z,y,x 181, 217, 181, steps 1,1,1)
rf-
bias field corrected file
sag3d-
original structural mri scan (unrotated, not cleaned)
seg-
segmented structural scan: 1= white matter, 2= gray matter, 3= csf
MEASURES
Gray matter density
Distance from center
Asymmetrey right vs left
Thickness measures
Correlations of age/gender/asym/brain volume/test
scores
GENERAL
The original reslice images
are in flipped space. Left hemisphere is in right space, right hemisphere
is in left space.
10/13/03
LINE
Line 16R for subject 106 was drawn incorrectly.
10/03
THICKNESS
An error was found where mincmath
was incorrectly extracting white matter from the segmented image. Though
not completely clear what was the problem, it can be fixed by rerunning
the bad subjects again with a larger range for white matter values in the
pipeline. The affected subjects are (left hem only): 101 113 115 121 125
139 141 142 147 14 151 152 153 155 159 164 167 175 176 177 178 180 184
195 197 199 19 200 203 204 206 208 209 20 210 212 213 216 22 30 36 39 40
45 51 53 54 57 61 62 63 64 69 74 77 80 87 90 92 96 97
9/03
THICKNESS
In order to keep the transformations
the same between thickness and density, the sameness in the order of the
transformations is very important!
In pipeline, it was found the
order of the lists were inconsistent with each other. This was fixed by
simply renaming the files to their correct subjectid names. The script
can be found here: /loni/edevel/YALE_THICKNESS/SCRIPTS/ERROR_CORRECTION