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mkbrainmask-sess - mask brain |
mkbrainmask-sess - make brain mask using ["BET"] |
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mkbrainmask-sess-s [sessid] or -sf [sessidfile] -d [srchdir] or -df [srchdirfile] [<options>] |
mkbrainmask-sess -s [sessid] -d [srchdir] [<options>] [[BR]] mkbrainmask-sess -sf [sessidfile] -df [srchdirfile] [<options>] |
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|| -fsd [funcsubdir] || functional subdirectory (default: bold) || || -run [nth] || use the nth run (default is 1st) || || -thresh [threshold] || fraction of global mean to separate brain and air (default is .1) || || -maskstem stem || stem of binary mask (stored in fsd/masks/stem) default is brain || || -help || print help and exit || || -version || print version and exit || |
|| -fsd [funcsubdir] || functional subdirectory (default: bold) || || -run [nth] || use the nth run (default is 1st) || || -thresh [threshold] || fraction of global mean to separate brain and air (default is .1) || || -maskstem stem || stem of binary mask (stored in fsd/masks/stem) default is brain || || -help || print help and exit || || -version || print version and exit || |
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This program creates a binary mask of the brain given an input functional volume. It uses the FSL (www.fmrib.ox.ac.uk/fsl) Brain Extraction Tool (BET). By default, the input is the f volume from the first run of the session from the bold directory. The input volume can be changed with the -funcstem option; the run can be changed with the -run option; and the functional subdirectory can be changed with the -fsd option. The output will be placed in a directory called masks under the FSD. The stem will be brain unless changed with the -maskstem option. The only real parameter is the threshold (controlled with the -thresh option). The absolute threshold is set to thresh times the global mean. |
mkbrainmask-sess creates a binary mask of the brain from an input functional volume. It uses the ["FSL"] Brain Extraction Tool (["BET"]). By default, the input is the f volume from the first run of the session from the bold directory. The input volume can be changed with the -funcstem option; the run can be changed with the -run option; and the functional subdirectory can be changed with the -fsd option. The output will be placed in a directory called masks under the FSD. The stem will be brain unless changed with the -maskstem option. The only real parameter is the threshold (controlled with the -thresh option). The absolute threshold is set to thresh times the global mean. |
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inorm-sess foo -i f -o out | mkbrainmask-sess foo -i f -o out |
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inorm-sess foo -i f -o out -f fvalue | mkbrainmask-sess foo -i f -o out -f fvalue |
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["spatialsmooth-sess"] | ["othercommand1"] |
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FsFast | FsFast, ["FSL"], SkullStripping |
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description description |
A brain mask was generated using the Brain Extraction Tool (BET) which is available from the FSL software library (www.fmrib.ox.ac.uk/fsl) (Smith 2002). |
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References/NameYear | ["References/Smith2002"] |
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Those using this program should cite: Smith, S. (2000). Robust automated brain extraction. NeuroImage. Submitted. |
DougGreve |
Name
mkbrainmask-sess - make brain mask using ["BET"]
Synopsis
mkbrainmask-sess -s [sessid] -d [srchdir] [<options>] BR mkbrainmask-sess -sf [sessidfile] -df [srchdirfile] [<options>]
Positional Arguments
None
Required Flagged Arguments
-s [sessid] or -sf [sessidfile] |
description |
-d [srchdir] or -df [srchdirfile] |
description |
Optional Flagged Arguments
-fsd [funcsubdir] |
functional subdirectory (default: bold) |
-run [nth] |
use the nth run (default is 1st) |
-thresh [threshold] |
fraction of global mean to separate brain and air (default is .1) |
-maskstem stem |
stem of binary mask (stored in fsd/masks/stem) default is brain |
-help |
print help and exit |
-version |
print version and exit |
Outputs
volume1 |
description |
Description
mkbrainmask-sess creates a binary mask of the brain from an input functional volume. It uses the ["FSL"] Brain Extraction Tool (["BET"]). By default, the input is the f volume from the first run of the session from the bold directory. The input volume can be changed with the -funcstem option; the run can be changed with the -run option; and the functional subdirectory can be changed with the -fsd option. The output will be placed in a directory called masks under the FSD. The stem will be brain unless changed with the -maskstem option. The only real parameter is the threshold (controlled with the -thresh option). The absolute threshold is set to thresh times the global mean.
Example 1
mkbrainmask-sess foo -i f -o out
description
Example 2
mkbrainmask-sess foo -i f -o out -f fvalue
description
See Also
["othercommand1"]
Links
FsFast, ["FSL"], SkullStripping
Methods Description
A brain mask was generated using the Brain Extraction Tool (BET) which is available from the FSL software library (www.fmrib.ox.ac.uk/fsl) (Smith 2002).
References
["References/Smith2002"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>