There is not much documentation about possum.
Part of FSL (build 509)
pulse
Copyright(c) 2003, University of Oxford (Ivana Drobnjak and Mark Jenkinson)
Usage:
pulse -i <input digital brain> -o <output base name> [optional arguments]
Compulsory arguments (You MUST set one or more of):
-i,--inp 4D digital brain, resolution can be any.
-o,--out pulse sequence matrix
Optional arguments (You may optionally specify one or more of):
--seq default=epi (epi OR ge)
--angle default=90 (flip angle in degrees)
--te default=0.03s (the time from the first RF to the first echo (in epi center of the k-space, in GE it is the center of the first line of the k-space)
--tr default=3s (the time between the two RF pulses applied on the same part of the object (in epi the acquisition time for the whole k-space in GE time for the first line)
--trslc default=0.12s (the time that takes for the acquisition of one slice)
--nx default=64 (resolution in x of the output image)
--ny default=64 (resolution in y of the output image)
--dx default=0.004m (image voxel x-dimension)
--dy default=0.004m (image voxel y-dimension)
--maxG default=0.055 T/m (maximum gradient strength)
--riset default=0.00022s (time it takes for the gradient to reach its max value)
--bw default=100000Hz ( receiving bandwidth)
--numvol default=1 (number of volumes)
--numslc default=1 (number of slices)
--slcthk default=0.006m (slice thickness)
--gap default=0m (gap between the slices in m)
--zstart default=0m (the lowest position in the slice direction in m)
--slcdir default=z- (x+,x-, y+,y- or z+,or z- slice acquisition direction/orientation)
--phasedir default=y+ (x+,x-, y+,y- or z+,or z- phase encode direction/orientation)
--readdir default=x+ (x+,x-, y+,y- or z+,or z- read-out direction/orientation)
-v,--verbose switch on diagnostic messages
-h,--help display this message
-k,--kcoord default=no (saving k-space coordinates)
--cover default=100 (phase partial Fourier coverage in %. min=50 max=100)
Usage: possumX <subject directory> [options]
Subject directory needs to contain:
1. brain
2. MRpar
3. motion
4. slcprof
5. pulse, pulse.info, pulse.readme, pulse.posx, pulse.posy, pulse.posz
optional
6. T2
7. T2timecourse
8. b0z_dz and (in case of motion) b0x_dx, b0x_dy, ... b0z_dy
9. b0extra
10. b0timecourse
In case there is a cluster enviroment (e.g. SGE):
-n (number of processors, default 1)
-t (estimated running time per processor (minutes), default 2000)
-s (marix segment size [default 10000], purely for memory efficiency)
-a (architecture [e.g., darwin or lx24-amd64])
-v verbose
-j (place hold for till this job finishes)Part of FSL (build 509)
possum (Version 2.0)
Copyright(c) 2008, University of Oxford (Ivana Drobnjak)
Usage:
possum_matrix -p <pulse> -m <motion file> -o <output main even matrix> [optional arguments]
Compulsory arguments (You MUST set one or more of):
-m,--motion <inputmatrix-filename> (Motion matrix [time(s) Tx(m) Ty(m) Tz(m) Rx(rad) Ry(rad) Rz(rad)])
-p,--pulse <inputmatrix-basename> (Pulse sequence - all additional files .posx,.posy, etc, expected to be in the same directory)
-o,--mainmatx <outputmatrix-filename> (Main event matrix [t(s),rf_ang(rad),rf_freq_band(Hz),(4)=rf_cent_freq(Hz),read(1/0),Gx,Gy,Gz(T/m),Tx,Ty,Tz(m),angle_of_rot B(rad),rot_axis Bx,By,Bz(m),angle_of_rot A(rad),rot_axis Ax,Ay,Az(m)])
Optional arguments (You may optionally specify one or more of):
-v,--verbose switch on diagnostic messages
-h,--help display this message
--old Allows for the old version of the sorter to run
--seg Seting the size of the segment of the matrix that is read in one at a timefsl_sub V1.1 - wrapper for job control system such as SGE
Usage: fsl_sub [options] <command>
fsl_sub gzip *.img *.hdr
fsl_sub -q short.q gzip *.img *.hdr
fsl_sub -a darwin regscript rawdata outputdir ...
-T <minutes> Estimated job length in minutes, used to let SGE select
an appropriate queue
-q <queuename> Possible values for <queuename> can be queried with
'qconf -sql'
-a <arch-name> Architecture [e.g., darwin or lx24-amd64]
-p <job-priority> Lower priority [0:-1024] default = 0
-M <email-address> Who to email, default = root@localhost
-j <jid> Place a hold on this task until job jid has completed
-t <filename> Specify a task file of commands to execute in parallel
-N <jobname> Specify jobname as it will appear on queue
-l <logdirname> Where to output logfiles
-m <mailoptions> Change the SGE mail options, see qsub for details
-z <output> If <output> image or file already exists, do nothing and exit
-F Use flags embedded in scripts to set SGE queuing options
-s <pename>,<threads> Submit a multi-threaded task - requires a PE (<pename>) to be
configured for the requested queues.
<threads> specifies the number of threads to run
-v Verbose mode.Part of FSL (build 509)
possum_sum
Copyright(c) 2006, University of Oxford (Ivana Drobnjak)
Usage:
possum_sum -i <inname> -o <outname> -n <nproc>
Compulsory arguments (You MUST set one or more of):
-i,--in input signal for one processor (possum output matrix)
-o,--out output signal: sum of all the processors (possum matrix form)
Optional arguments (You may optionally specify one or more of):
-n,--nproc Number of processors
-h,--help display this message
-v,--verbose switch on diagnostic messagesPart of FSL (build 509)
signal2image
Copyright(c) 2003, University of Oxford (Mark Jenkinson & Ivana Drobnjak)
Usage:
signal2image [options] -i <signal> -p <pulse> -o <image>
signal2image -p <pulse> -c <kcoord>
Compulsory arguments (You MUST set one or more of):
-p,--pulse 8-column pulse_sequence matrix. Expects to find all other pulse sequence files in the same directory.
Optional arguments (You may optionally specify one or more of):
-i,--in input signal
-o,--out output image
-c, --kcoord kspace coordinates
-k,--kout output k-space
-a,--abs save absolute magnitude and phase
--homo do the homodyne reconstruction
-v,--verbose switch on diagnostic messages
-h,--help display this message
-z,--apodize Do apodization
-l,--limit Apodization with this cutoff; default 100
-r,--roll Apodization with this rolloff; default 10
-s,--save (DEBUG!) Save window as ascii matrix