#################################################
#################################################
 This is the default template for UCSD NOTES
 files.  The functional and subject versions of
 this file ($session/image/scripts/NOTES and 
 $subject/scripts/NOTES) can be retrieved with
 Alt-n, or with the corresponding File->NOTES
 menus.  Ideally, paper scanning notes should be
 transcribed (and these lines deleted!!) at the
 time that a set of scan is first unpacked.
#################################################
#################################################



#################################################
6/1/02 -- struct scan example: 2 sagittal MPRAGEs
#################################################
# transcribe session notes from paper
flip avoid:    vitamin E capsule right cheek
subject name:  marty
patient num:   2517
slice plane:   SAG
pixel size:    1x1x1 mm
slice count:   180

# backup raw data to CDROM
CDROM made

# add new subject to database
File -> New Subject

# copy raw files into blank subject dir
cd $SUBJECTS_DIR/sabrina/mri/orig
mkdir mprage1 mprage2
set rawftpdir = /tmp/cdrom17/sabrina
cp $rawftpdir/2517-2-*.ima mprage1
cp $rawftpdir/2517-3-*.ima mprage2

# basic surface reconstruction, sphere align
SubjectTools -> Setup Structural Scans
  [align MPRAGE's; sag->cor flip: -z y x]
SubjectTools -> Process/Create/Fix/Final (1 day)
  [Edit Segmentation, redo Create/Fix/Final]
SubjectTools -> Make Full Surface Cuts
SubjectTools -> Flatten Surface (1 day)
SubjectTools -> Register Surface (1 day)

# notes on state of reconstruction 
...
...
...
...


#################################################
6/1/02 -- funct scan session example: retin/faces
#################################################
# add new session to database
File -> New Functional -> 020605MS
 (format: Year-Month-Day-Initials format)

# setup notes
subject name:      marty
video sets:        upside down
screen setup:      Boynton, nose blocker, bitebar
RF coil:           small flex, placed low
slice plane:       COR
voxel:             3x3x4
slices:            26
reps:              130
funct shiftmean:  -61.6mm
struct shiftmean:  0.0 mm
backup:            CDROM made

# stimulus notes
 --retinotopy and faces

# goto image dir
cd $FUNCTIONALS_DIR/020605MS/image

# symbolic link to raw data dir
ln -s \
  /kamares/usr1/tmp/ftpscan/cdrom75/020605MS raw

# run countem to check bounds
newdefs
countem raw
-------------------------------------------------
1643-2  130  4 ->    133   512x512 imgs   530432
1643-3  130  134 ->  263   512x512 imgs   530432
1643-4  130  264 ->  393   512x512 imgs   530432
1643-5  130  394 ->  523   512x512 imgs   530432
1643-6  240  524 ->  763   256x256 imgs   137216
-------------------------------------------------

# unpack/convert/autonumber scans into named dirs
convertem ecc1 pol1 pol1 faces mprage

 => generates
      image/1-ecc1/ecc1-1+orig.BRIK
      image/2-pol1/pol1-1+orig.BRIK
      image/3-pol1/pol1-2+orig.BRIK
      image/4-faces/faces-1+orig.BRIK
      image/mprage/COR-

