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Manpage of cpstats
cpstats
Section: User Commands (1)
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NAME
cpstats - Does statistics on PICo maps.
SYNOPSIS
cpstats
-inputroot <root> -operation <min |
max | median | mean> -outputroot <root> [-pd <p>]
[-targetindex <index>]
DESCRIPTION
This program performs simple voxelwise operations on a series of
images. The min, max, median, mean or sum in each voxel in the series
of images is computed and written to a single image.
This program and its wrappers will work with any scalar Analyze images, including
un-normalized streamline counts from procstreamlines.
EXAMPLES
Track from an ROI in the brain, defined by a seed image (see
track(1)), and get the maximum connection probability from any ROI
seed to each voxel in the image.
cat A.inv1.watson.Bdouble | track -seedfile roi.hdr -watson |
procstreamlines -seedfile roi.hdr -outputcp -outputroot A_oneDT_
The seed file contains a single ROI, marked as voxels with value 1, so
the input is A_oneDT_watson_nonInt_1_[1...N]_1.hdr, where N is the
number of seeds in the ROI. To find the maximum connection probability
from the ROI to any voxel, use cpstats:
cpstats -inputroot A_oneDT_watson_nonInt_1_ -operation max -outputroot
maxroicp
This creates the Analyze image maxroicp.[hdr,img].
OPTIONS
- -inputroot <root>
-
File root for the input. The input images must be in the same
directory and be numbered. The program will look for root1_P.[img
| img.gz], root2_P.[img | img.gz], until there are no more seeds. The index
P is the principal direction that the tractography follows at the seed point. The
default is P=1 unless otherwise specified with the -pd option.
- -operation <operation>
-
The operation to perform. Either min for the minimum value in
each voxel across all images, max for the maximum, mean,
median or sum.
- -outputroot <file>
-
File root for the output, in Analyze format. Defaults to the operation
name, so if this is not specified and the operation is max, then the
output will be maxcp.[hdr,img]. For legacy compatibility, the -outputfile
option does the same thing as -outputroot.
- -pd <p>
-
Each principal direction in the seed ROI is given its own connection probability map
by procstreamlines. This option tells cpstats over which PD to compute the
statistic. The default is 1. Older versions of Camino outputted connection probability
maps from track, and no PD was specified in the output file names. If no PD index
is detected in the input files, then this argument is ignored.
If this option is specified, then the tractography results for PD 1 must be present
in the same directory. For each volume corresponding to PD 1 that the program finds,
it will look for a volume for PD p.
- -targetindex <index>
-
Target connection probability images have an extra suffix (_0 or _1) to record whether the
image corresponds to tracking against or with a specified direction. The index 0 or 1 should
be specified when computing statistics on target connection probability images.
AUTHORS
Philip Cook <camino@cs.ucl.ac.uk>
SEE ALSO
track(1), picopdfs(1)
BUGS
When there are multiple principal directions in a voxel, the PDs 1 through N are not
ordered by Camino programs. For example, if an ROI is placed in a region where two fibre
bundles cross, then PD 1 at seed 1 may point along the same fibre bundle as PD 2 in seed 2.
The only way to ensure that a PD index corresponds to the same fibre bundle across multiple seeds
is to visually inspect and order the connection probability maps.
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- EXAMPLES
-
- OPTIONS
-
- AUTHORS
-
- SEE ALSO
-
- BUGS
-
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