-M scalar intensity multiplier
-T slice thickness (for Analyze output)
-A Analyze 3D format. Follow by slice thickness
-# number of slices in 'mdisplay' format for infile
-t separate file for each time point
-s separate file for each slice
-N Normalize full range of input intensities to full range of output type
-m F-L save output files in mdisplay format (multiple slices/image)
F and L are the first and last slice for mdisplay
The option '-m A' will use all slices
-R Auto window input intensities to full range of output type
-e emulate epi2bshort (but without offset artifacts!)
-f force output type to float for Analyze files
-F flip image top and bottom
-V verbose operation
saves a processing file "outFile.imconvert.proc"
e.g.> imconvert -i /apd6/anmr_scans/image/foo_0004_0001_001.img -o HRa.bshort -m 1-26
This will give you a bshort to look at from which you can pick your slices, and go back and rerun imconvert
with new values in the -m option
[[THIS IS NO LONGER NEEDED/USED]]
-->mdisp
Usage: mdisp *inflies option
GRIND IT
This step is the statistical analysis on the raw functional data
-->Cproto
Cproto is an interactive program.
There is extensive help on it, but basically for CC_gr you need to input a
1 or 0 for each scan(TR) you did.
If you started out with 10 scans of rest then had 10 scans of
activation:
10,0
10,1
You will need to put a finishing 0 on a new line after you finish
entering.
-->CC_gr
Usage: CC_gr -i input_file -o output_file (basename) -p
paradigm_file
[ -G global normalization -R normalization_ratio_file
-F Change to Light Speed (real-time mode enabled)
-V verbose
-K Smoothing
-N noise_threshold
-Q create quicklook (.covl and .sovl) files
-L t cutoff for slope and quicklook map
-U upper limit of t displayed in quicklook maps
-b bshort multi-display file (for time series)
-G global normalization
-R normalization_ratio_file
-v output as volume format (may be useful for MedX) ]
The first three arguments are required.
Auto thresholding is ON by default, use -N 0 to override
Outputs a processing record: outputname.CC_gr.proc
CC_gr -h prints an extensive (out of date) help file
e.g.> CC_gr -i /apd6/.../foo_0004_0002_001.img -o run1_object -p
Cproto.output -G -K -N 200 -b
DISPLAY IT
-->xds/xdd
These two programs will allow you to display your data on the UNIX
machines, without, or with color respectively.
Usage:xds [-z ] [-r ] [-hqMPRI] filename
[-A ]
[-v ] [-m ] [-l ]
[-L ] [-H ]
[-s ] [-# ] [-e ]
[[-s ] [-e ] [-# ] ] ...
[-b] bilinear interpolation mode.
[-z ] Increase image size by a factor of in linear dimensions.
[-r ] Make the pixels times larger in the vertical
direction.
[-h] Print help information. (Same as 'h' key).
[-q] Toggle quiet mode (don't print statistics). (Same as 'Q' key).
-[M]|[P]|[R]|[I] Define data as complex and select mag, phase, real,
or imaginary. (Same as '1 D', '2 D', '3 D', and '4 D' respectively.)
[-A ] Filename for statistical image (KS_grinder or T_grinder
output)
[-v ] Filename for overlay data (ascii x,y pairs) or seg .otl file.
[-m ] Filename to load 256 ascii triples as 0-65535 rgb color map.
Data file then must vary only [0..255], interpreted as
colors.
[-l ] Filename to save log data into (output of 's' command).
[-W] Auto window and level each window individually (for disparate
images).
[-L ],[-H ] User-defined data limits to force image
contrast.
Data outside this range will be displayed as black or white.
[-s ] Start loading at image , where n starts at 0.
[-# ]|[-e ] Load the following file for images or at image .
Image stack filenames, named with appropriate extension;
Input files must be acceptable to read_image(), or ANMR .im files.
N.B. The -s, -e, -# parameters apply only to SUBSEQUENT files, and until
replaced. e.g. xds -s 0 -# 10 f1.bshort -s1 -#10 f2.bshort
reads 20 images, but the second -#10 is redundant.
e.g.: xds run1_object.bfloat
e.g.: xdd run1_object.buchar
PRINT IT
-->overlay
This will overlay the functional correlation maps onto a HiRes EPI
image.
Usage: overlay -B baseimage -O overlayimage -o outputname
-[u,l,U,L,d,#,N,V]
REVISED 12/4/96 -- Please report any errors to Mark Cohen
Takes two images, (base and functional) and forms a composite
with the functional containing the upper gray scale values. The
overlay image is interpolated, if needed, to the base image size.
The output image is an eight bit Mac-compatible file
The current version shows positive and negative overlays by default
and uses pixel replication (rather than interpolation) for overlays
Note new options for slice and image.
OPTIONS:
B: baseimage (REQUIRED)
u,l: upper & lower range for baseimage
(default: automatic noise threshold detection)
O: overlayimage (REQUIRED)
U,L: upper & lower range for overlay
(defaults: half of overlay max to max)
N.B. -U and -L are REQUIRED for multi image sets
s: Only use positive intensities in overlay
o: Output file (REQUIRED). Basename only; type will be buchar
#: Image number to use from overlay set (counting from one)
S: Slice number to use from multi-slice base set (counting from one)
N: Image number to use from multi-image base set (counting from one)
I: Bilinear Interpolation (default is replication)
h: Prints out an extensive help file.
V: verbose option
Outputs a processing record: outputname.overlay.proc
e.g.: overlay -B HR.bshort -O run1_object.bfloat -o Someone_object -# 1
-l 0 -u 600 -L .3 -U 1.2
Then you want to pull it to a mac...
AIR IT
This step is if you see you have a lot of motion and you want to try to
correct for it
-->AIR
This step will motion correct raw files, then you need to re-run through
the above steps.
Usage:AIR inputname outputname numimages interplanedist threshold
res referencetimepoint deleteworkingfiles firstslice lastslice
refvolume
where inputname = blah_00001_00001_001, raw ANMR data, do not put .img
outputname = outputfilename, it defaults to .bshort, so do not put it
numimages = number of 3-D data sets in time series
interplanedist = slicethickness (eg 4) + interslicespacing (eg 1)
(default = 5)
threshold = noise threshold, recommended >=160 (default)
res = 64 for 64 x 64(default), 128 for 128 x 128, 0 no cropping
referencetimepoint = 1 (default) to align to 1st volume, 20 to 20th
volume, etc.
deleteworkingfiles = y (default), n
firstslice = 0 (default, take all slices in mdisp) or slice to start
with mdisp
(eg. 2, to skip 1st slice lost in motion correction)
lastslice = 0 (default, take all slices), or last slice to take in
mdisp
referencevolume = filename for external volume to align to (eg. to
align to another run)
This overrides referencetimepoint
Description: Takes raw ANMR data and outputs AIRed (v. 3.03) bshort data
Notes:
1) Make sure NOT to include '.img' or '.bshort' in 'inputname' or
'outputname'
2) Place no periods in outputname
3) All output files will be in the CURRENT WORKING DIRECTORY (i.e. pwd).
Do NOT specify any directory paths in 'outputname'
Input files may have a directory specification
4) A bunch of working files are created, so you may want to create a
working directory
and run this script from there, so as not to clutter your directory.
5) Overwrite permission is not enabled.
6) AIR deletes all working files, except the .air files which are tarred
into an archive.
If you specify n for delete working files, AIR will preserve the
resliced .bshort timeseries for each slice.
7) So as not to oeverload the machine, especially when you are going to
align several datasets at once in the background, use the nice command
(see example)
Example 1: If the file to be aligned is in the current directory,
mkdir align
cd align
nice AIR ../test_00717_00005_00001_00001_001 testaligned 216 5
Example 2: For 100 images, 3mm/0skip slices, threshold 160, matrix
128x128, will align to the 50th image,
keep slices 2-10 in the mdisp, and preserve working
files:
nice AIR ../blah_001 testout 100 3 160 128 50 n 2 10
Example 3: This will do the same except align to an external reference
volume:
nice AIR ../blah_001 testout 100 3 160 128 1 n 2 10 otherrun
A .proc file is output
e.g.: AIR /apd6/.../foo_00004_00002_001 run1_aired_object 84 5 160 64
42
This will run as long as you give it input and output and timepoints, all
reast will default. reference time point is one i often change in order to
AIR to the middle image (better for correction)
*You should make a new sub_directory for this, and then work out of
there.
Pix
stay tuned...
this page is maintained by fred [12.1.99]