Home – PyHRF

PyHRF is a Python library for the analysis of fMRI data based on the study of hemodynamics.


Configuration – Package options are stored inĀ $HOME/.pyhrf/config.cfg, which is created after the installation.


It handles global package options and the setup of parallel processing. Here is the default content of this file (section order may change):

write_texture_minf = False          ; compatibility with Anatomist for texture file
tmp_prefix = pyhrftmp               ; prefix used for temporary folders in tmp_path
verbosity = 0                       ; default of verbosity, can be changed with option -v
tmp_path = /tmp/                    ; where to write file
use_mode = enduser                  ; "enduser": stable features only, "devel": +indev features
spm_path = None                     ; path to the SPM matlab toolbox (indev feature)

[parallel-cluster]                  ; Distributed computation on a cluster.
                                    ; Soma-workflow is required.
                                    ; Authentification by ssh keys must be
                                    ; configured in both ways (remote <-> local)
                                    ; -> eg copy content of ~/.ssh/id_rsa.pub (local machine)
                                    ;    at the end of ~/.ssh/authorized_keys (remote machine)
                                    ;    Also do the converse:
                                    ;    copy content of ~/.ssh/id_rsa.pub (remote machine)
                                    ;    at the end of ~/.ssh/authorized_keys (local machine)

server_id = None                    ; ID of the soma-workflow-engine server
server = None                       ; hostname or IP adress of the server
user = None                         ; user name to log in the server
remote_path = None                  ; path on the server where data will be stored

[parallel-local]                    ; distributed computation on the local cpu
niceness = 10                       ; niceness of remote jobs
nb_procs = 1                        ; number of distruted jobs, better not over
                                    ; the total number of CPU
                                    ; 'cat /proc/cpuinfo | grep processor | wc -l' on linux
                                    ; 'sysctl hw.ncpu' on MAC OS X
                                    ; Set it to 0 if you want to auto-detect the number of
                                    ; availables cpus and cores (taking into account the kernel
                                    ; restrictions such as cgroups, ulimit, ...)

[parallel-LAN]                      ; Distributed computation on a LAN
                                    ; Authentification by ssh keys must be
                                    ; configured
remote_host = None                  ; hostname or IP address of a host on the LAN
niceness = 10                       ; niceness for distributed jobs
hosts = $HOME/.pyhrf/hosts_LAN      ; plain text file containing coma-separated list of hostnames on the LAN
user = None                         ; user name used to log in on any machine
                                    ; on the LAN
remote_path = None                  ; path readable from the machine where
                                    ; pyhrf is launched (to directly retrieve
                                    ; results)

Ramon Sanders

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