MVPA-PREP-FMRI(1) User Commands MVPA-PREP-FMRI(1)NAME
mvpa-prep-fmri - preprocess fMRI data for PyMVPA
SYNOPSIS
mvpa-prep-fmri [OPTIONS] <fmri-data>
DESCRIPTION
Tiny tool to prepare a directory for a typical analysis of fMRI data with PyMVPA. Tools from the FSL suite will be used for preprocessing.
It takes a 4D fMRI timeseries as input and performs the following steps:
- extract an example volume
- perform motion correction using the example volume as reference
- conservative skull-stripping and brain mask generation
- masking of the motion-corrected timeseries with the brain mask
All results will be stored either in the current directory, or in a subdirectory with the subject ID (if specified).
OPTIONS --version
show program's version number and exit
-v VERBOSE, --verbose=VERBOSE, --verbosity=VERBOSE
Verbosity level of output
-h, --help, --sos
Show this help message and exit
-s SUBJ, --subject-id=SUBJ
Subject ID used as output path
-e EXFUNC, --example-func-vol=EXFUNC
Volume (numeric ID or 'last', 'first', 'middle') to be used as an example functional image. Default: 10
-m MCFLIRT_OPTS, --mcflirt-options=MCFLIRT_OPTS
Options for MCFLIRT. '-plots' is auto-added
-p, --mcflirt-plots
Create a .pdf with plots of motion parameters
-b BET_OPTS, --bet-options=BET_OPTS
Options for BET. '-m' is auto-added. Default: '-f 0.3' for a safe guess of the brain outline
mvpa-prep-fmri 0.4.8 April 2012 MVPA-PREP-FMRI(1)
Check Out this Related Man Page
MAKE-PLOTS(1) User Commands MAKE-PLOTS(1)NAME
make-plots - Plots histograms in FLAT format
SYNOPSIS
make-plots [options] file.dat [file2.dat ...]
OPTIONS -h, --help
show this help message and exit
-n NUM_THREADS, -j NUM_THREADS, --num-threads=NUM_THREADS
max number of threads to be used [8]
--palatino
Use Palatino as font (default).
--cm Use Computer Modern as font.
--times
Use Times as font.
--minion
Use Adobe Minion Pro as font. Note: You need to set TEXMFHOME first.
--ps Create PostScript output (default).
--pdf Create PDF output.
--eps Create Encapsulated PostScript output.
--png Create PNG output.
--pspng
Create PS and PNG output.
--pdfpng
Create PDF and PNG output.
--epspng
Create EPS and PNG output.
--tex Create TeX/LaTeX output.
--no-cleanup
Keep temporary directory and print its filename.
--full-range
Plot full y range in LogY plots.
-c CONFIGFILES, --config=CONFIGFILES
Plot config file to be used. Overrides internal config blocks.
-v, --verbose
print debug (very verbose) messages
-q, --quiet
be very quiet
AUTHOR
This manual page was written by Lifeng Sun <lifongsun@gmail.com> for the Debian system (but may be used by others).
Rivet June 2012 MAKE-PLOTS(1)
Hi i have encountered a problem and i have tried many different things but my brain just has some limitations lol well anyways i was trying to make this program work down below so i can process multiple commands just by separating them with ;. I would apeciate if someone could just make it work kuz... (2 Replies)
Hi there,
I realize this may not be directly related to Unix, but I have recently been using an fMRI analysis program called FreeSurfer which is primarily run in the tclsh shell. However, I have been unable to open up the GUI, and I get the following error message when I attempt to do so:
... (0 Replies)
Ive been looking through various exam prep sites (testking.com,testking.net, testking.org, and pass4sure.com) and im having trouble deciding on one. If anyone has purchased any of these products (or a similar one) please let me know what you thought of it. I would prefer a course with practice... (1 Reply)