Name

mri_surfcluster

Description

This tool allows you to cluster surface data. This program assigns each vertex on a cortical surface to a cluster based on the distribution of intensity values in the source file. A vertex must meet two criteria to be part of a cluster. First, its intensity must fall within a certain range (the intensity threshold criteria). Second, it must be part of a contiguous set of vertices that meet the threshold criteria and whose surface area is greater than a minimum.

There are three types of output. (1) Summary file - simple text file with a list of clusters found including maximum value, area, and talairach coordinate. (2) Filtered - identical to the input except that vertices not assigned to a cluster are set to 0. (3) Cluster number surface - this has the same format as the input and filtered output except that the value at each vertex is the cluster number assigned to it.

Synopsis

mri_surfcluster --in <in file> [options]

Arguments

Flag	Description
--in inputfile	This is the input data to the clustering program. Reads all formats supported by mri_convert.
--subject subjectid	Surface values are defined on this subject.
--hemi hemi	Specify the cortical hemisphere that the input represents. Valid values are lh and rh.
--surf surface	This is the surface to use when computing the talairach coordinates. Default is white.
--annot annotationname	Report the cortical annotation that the maximum in each label falls into. The annotation used will be SUBJECTS_DIR/subject/label/hemi.annotationname.annot. Eg, --annot aparc
--frame frameno	Zero-based frame number of the input file. Default is 0. For paint format, zero is the only possible value.
--thmin minthresh	Minimum threshold in the intensity threshold criteria. Vertices on the surface are excluded or included, in part, based on their intensity. For a vertex to be included, its value (ie, intensity) must be within a certain range (namely, between the minimum threshold, set with --thmin, and the maximum threshold, set with --thmax). While thmin and thmax must be positive values, the sign of the threshold can be set with --thsign. However, if thmax is negative, then the maximum threshold will be set to infinity. For example, if --thmin 2 --thmax 5 --thsign pos, then all vertices with values between (positive) 2 and 5 will be candidates for clustering. However, if --thsign abs is used instead, then all vertices between -2 and -5 as well as between +2 and +5 will be candidates.
--thmax maxthresh	Maximum threshold in the intensity threshold criteria. If negative, then the maximum threshold is infinity. See SETTING THE CLUSTER INTENSITY THRESHOLD CRITERIA below.
--sign threshold sign	This is used to control the sign of the threshold criteria. Legal values are pos, neg, and abs. See SETTING THE CLUSTER INTENSITY THRESHOLD CRITERIA below.
--no-adjust	Do not adjust thresh for one-tailed tests. By default, the threshold will be adjusted when the --sign is pos or neg by subtracting log10(2.0). This assumes several things: (1) the source is a -log10(p) map, and (2) the pvalue was computed using a two-sided t-test. Under these conditions, subtracting log10(2.0) is like dividing the p-value by 2 (ie, changing it from a two-tailed test to a one-tailed test). If the input map does not meet these criteria, then run with --no-adjust.
--fdr FDR	Set thmin with False Discovery Rate. 0 < FDR < 1. Usually something like .01 or .05. Only when input is -log10(p).
--csd csdfile <--csd csdfile>	Load one or more CSD files. CSD stands for 'Cluster Simulation Data'. This file is produced by running mri_glmfit with --sim. The the threshold and hemi info are obtained from the CSD file and cannot be specified on the command- line. If more than one CSD is specified, they are merged into one CSD internally. When a CSD file is specified, three more columns are added to the summary table: 1. CWP - cluster-wise pvalue. The pvalue of the cluster corrected for multiple comparisons 2. CWPLow - lower 90% confidence limit of CWP based on binomial distribution 3. CWPHi - upper 90% confidence limit of CWP based on binomial distribution
--cwsig cluster-wise_map	Saves the sigificance map of the clustersthe clusters in which the value of each vertex is the -log10(pvalue) of cluster to which the vertex belongs (the cluster-wise significance). The user can also specify that the vertex-wise significance be computed and saved with --vwsig. The significance is based on the distribution of the maximum significances found during the CSD simulation.
--csdpdf csdpdfile	Compute PDF/CDF of CSD data and save in csdpdffile. This is mostly good for debugging.
--csdpdf-only	Only write the csd pdf file.
--minarea area	Minimum surface area (in mm^2) that a set of contiguous vertices must achieve in order to be considered a cluster.
--clabel labelfile	Constrain cluster search to be inside or outside clabel. By default, it will be constrained to be INSIDE. For OUTSIDE, specify --clabelinv. clabel must be a surface-based label.
--mask-inv	Constrain cluster search to be OUTSIDE mask or clabel.
--sum summaryfile	The summary text file (the argument of the --sum flag) will contain a summary of the result of the clustering as well as a summary of the conditions under which the clustering was performed. It will list the clusters (1 to N) along with the maximum value found in the cluster (Max), the vertex at which this maximum value was found (VtxMax), the surface area of the cluster (Size), and the Talaiarach coordinates of the maximum (based on talairach.xfm).
--o outputid	File in which to store the surface values after setting the non-cluster vertices to zero. Fmt is the format (currently, only paint format is supported). Note: make sure to put a ./ in front of outputid or else it will attempt to write the output to the subject's surf directory.
--ocn ocnid	File in which to store the cluster number of each vertex. This can be useful for determining to which cluster a particular vertex belongs. It can be viewed as with any other surface value file. Fmt is the format (currently, only paint format is supported). Note: make sure to put a ./ in front of outputid or else it will attempt to write the output to the subject's surf directory.
--olab outlabelbase	Save output clusters as labels. There will be a label file for each cluster. The name will be outlabelbase-XXXX.label, where XXXX is the 4-digit, zero-paded cluster number. The stat field in the label will be the value of the input statistic at that vertex.
--xfm xfmfile	This is a transform file that is used to compute the Talairach coordinates of a vertex for the summary file. The file must be found in subjects_dir/subjectid/transforms. The default is talairach.xfm which is based on the MNI atlas (see --fixmni).
--fixmni --nofixmni	Fix (or do not fix) MNI Talairach coordinates based on Matthew Brett's transform. See http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html. Default is to fix. The user may elect not to fix if the xfm file is not talairach.xfm (see --xfm).
--sd subjects_dir	This allows the user to change the FreeSurfer subjects's directory from the command-line. If unspecified, it will be set to the environment variable SUBJECTS_DIR

-  ⇤ ← Revision 6 as of 2004-12-21 18:13:50 → 
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-mri_surfcluster - This tool allows you to cluster surface data.
+mri_surfcluster
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+Line 15:
+= Description =
 Line 17:
-= Synopsis =
+This tool allows you to cluster surface data.
-Line 35:
+Line 34:
+= Synopsis =
mri_surfcluster --in <in file> [options]
-Line 37:
+Line 38:
-   --hemi hemi : lh or rh 
         Specify the cortical hemisphere that the input represents. Valid values
         are lh and rh.
#

   --src srcid <fmt> : source of surface values    
         Input data to the clustering program. Fmt is the format 
         specification. Currently, only paint format is supported.
#
   --srcsubj  subjid    : source surface subject (can be ico)
#      
   --srcsurf  surface   : get coorindates from surface (white)
         Surface to use when computing the talairach coordinates.
         Default is white.
#
   --srcframe frameno   : 0-based frame number
         Zero-based frame number of the input file. Default is 0. For paint
         format, zero is the only possible value.
#
   --thmin    threshold : minimum intensity threshold
         Minimum threshold in the intensity threshold criteria. See 
         setting the cluster intensity threshold criteria below.
#
   --thmax    threshold : maximum intensity threshold
         Maximum threshold in the intensity threshold criteria. If negative,
         then the maximum threshold is infinity.  See setting the cluster
         intensity threshold criteria below.
#
   --thsign   sign      : <abs>, pos, neg
         This is used to control the sign of the threshold criteria. Legal
         values are pos, neg, and abs. See setting the cluster intensity
         threshold criteria below.
#
   --minarea  area      : area threshold for a cluster (mm^2)
       Minimum surface area (in mm^2) that a set of contiguous vertices
       must achieve in order to be considered a cluster.
#
   --sum sumfile     : text summary file
       Text file in which to store the cluster summary. See Summary File Output below.
#
   --o outid <fmt>   : input with non-clusters set to 0
       File in which to store the surface values after setting the
       non-cluster vertices to zero. Fmt is the format (currently, only
       paint format is supported). Note: make sure to put a ./ in front
       of outputid or else it will attempt to write the output to the
       subject's surf directory.
#
   --ocn ocnid <fmt> : value is cluster number 
       File in which to store the cluster number of each vertex. This can be
       useful for determining to which cluster a particular vertex
       belongs. It can be viewed as with any other surface value file. Fmt is
       the format (currently, only paint format is supported). Note: make
       sure to put a ./ in front of outputid or else it will attempt to write
       the output to the subject's surf directory.
#
   --olab outlabelbase  : output clusters as labels 
       Save output clusters as labels. There will be a label file for each
       cluster. The name will be outlabelbase-XXXX.label, where XXXX is the
       4-digit, zero-paded cluster number. The stat field in the label will
       be the value of the input statistic at that vertex.
#
   --cht chtfile nithr ithrlo ithrhi ithrsign nsthr sthrlo sthrhi

   --xfm xfmfile     : talairach transform (def is talairach.xfm) 
       This is a transform file that is used to compute the Talairach 
       coordinates of a vertex for the summary file. The file must be
       found in subjects_dir/subjectid/transforms. The default is
       talairach.xfm which is based on the MNI atlas (see --fixmni).
# 
   --<no>fixmni      : <do not> fix MNI talairach coordinates
       Fix (or do not fix) MNI Talairach coordinates based on Matthew Brett's
       transform. See http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html.
       Default is to fix. The user may elect not to fix if the xfm file
       is not talairach.xfm (see --xfm).
#
   --sd subjects_dir : (default is env SUBJECTS_DIR)
      This allows the user to change the FreeSurfer subjects's directory
      from the command-line. If unspecified, it will be set to the 
      environment variable SUBJECTS_DIR
#
   --help : answers to ALL your questions
#
 
= Outputs =
   --sum sumfile     : text summary file
   --o outid <fmt>   : input with non-clusters set to 0
   --ocn ocnid <fmt> : value is cluster number 
   --olab labelbase  : output clusters as labels 

SUMMARY FILE OUTPUT

The summary file (the argument of the --sum flag) will contain a 
summary of the result of the clustering as well as a summary of the
conditions under which the clustering was performed. It will list
the clusters (1 to N) along with the maximum value found in the
cluster (Max), the vertex at which this maximum value was found
(Vtx Max), the surface area of the cluster (Size), and the Talaiarach
coordinates of the maximum (based on talairach.xfm). A sample 
summary file is shown below.

Cluster Growing Summary (mri_surfcluster)
$Id: mri_surfcluster.c,v 1.13 2004/10/19 23:32:42 greve Exp $
Input :      minsig-0-lh.w
Frame Number:      0
Minimum Threshold: 5
Maximum Threshold: infinity
Threshold Sign:    pos
Area Threshold:    40 mm^2
NClusters          37
Total Cortical Surface Area 115576 (mm^2)
FixMNI = 1

Cluster No   Max  Vtx Max  Size(mm^2)   TalX   TalY   TalZ
   1       44.6    6370    636.79    -33.6  -69.8   49.2
   2       40.3   48234    518.50     -2.9  -10.5   62.4
   3       39.5   54239    103.19    -51.1  -13.3   45.3
   4       39.5   55350     47.31    -50.1  -11.0   46.8




= Bugs =
Currently only supports paint (or w) format for input and output.
+|| Flag || Description||
|| --in inputfile || This is the input data to the clustering program.  Reads all formats supported by mri_convert. ||
|| --subject subjectid || Surface values are defined on this subject. ||
|| --hemi hemi || Specify the cortical hemisphere that the input represents. Valid values are lh and rh. ||
|| --surf surface || This is the surface to use when computing the talairach coordinates. Default is white. ||
|| --annot annotationname || Report the cortical annotation that the maximum in each label falls into. The annotation used will be SUBJECTS_DIR/subject/label/hemi.annotationname.annot. Eg, --annot aparc ||
|| --frame frameno || Zero-based frame number of the input file. Default is 0. For paint format, zero is the only possible value. ||
|| --thmin minthresh || Minimum threshold in the intensity threshold criteria. Vertices on the surface are excluded or included, in part, based on their intensity. For a vertex to be included, its value (ie, intensity) must be within a certain range (namely, between the minimum threshold, set with --thmin, and the maximum threshold, set with --thmax). While thmin and thmax must be positive values, the sign of the threshold can be set with --thsign. However, if thmax is negative, then the maximum threshold will be set to infinity. For example, if --thmin 2 --thmax 5 --thsign pos, then all vertices with values between (positive) 2 and 5 will be candidates for clustering. However, if --thsign abs is used instead, then all vertices between -2 and -5 as well as between +2 and +5 will be candidates.  ||
|| --thmax maxthresh || Maximum threshold in the intensity threshold criteria. If negative, then the maximum threshold is infinity. See SETTING THE CLUSTER INTENSITY THRESHOLD CRITERIA below.  ||
|| --sign threshold sign || This is used to control the sign of the threshold criteria. Legal values are pos, neg, and abs. See SETTING THE CLUSTER INTENSITY THRESHOLD CRITERIA below.  ||
|| --no-adjust || Do not adjust thresh for one-tailed tests. By default, the threshold will be adjusted when the --sign is pos or neg by subtracting log10(2.0). This assumes several things: (1) the source is a -log10(p) map, and (2) the pvalue was computed using a two-sided t-test. Under these conditions, subtracting log10(2.0) is like dividing the p-value by 2 (ie, changing it from a two-tailed test to a one-tailed test). If the input map does not meet these criteria, then run with --no-adjust.  ||
|| --fdr FDR || Set thmin with False Discovery Rate. 0 < FDR < 1. Usually something like .01 or .05. Only when input is -log10(p).  ||
|| --csd csdfile <--csd csdfile> || Load one or more CSD files. CSD stands for 'Cluster Simulation Data'. This file is produced by running mri_glmfit with --sim. The the threshold and hemi info are obtained from the CSD file and cannot be specified on the command- line. If more than one CSD is specified, they are merged into one CSD internally. When a CSD file is specified, three more columns are added to the summary table: 1. CWP - cluster-wise pvalue. The pvalue of the cluster corrected for multiple comparisons 2. CWPLow - lower 90% confidence limit of CWP based on binomial distribution 3. CWPHi  - upper 90% confidence limit of CWP based on binomial distribution  ||
|| --cwsig cluster-wise_map || Saves the sigificance map of the clustersthe clusters in which the value of each vertex is the -log10(pvalue) of cluster to which the vertex belongs (the cluster-wise significance). The user can also specify that the vertex-wise significance be computed and saved  with --vwsig. The significance is based on the distribution of the maximum significances found during the CSD simulation.  ||
|| --csdpdf csdpdfile || Compute PDF/CDF of CSD data and save in csdpdffile. This is mostly good for debugging.  ||
|| --csdpdf-only || Only write the csd pdf file.  ||
|| --minarea area || Minimum surface area (in mm^2) that a set of contiguous vertices must achieve in order to be considered a cluster.  ||
|| --clabel labelfile || Constrain cluster search to be inside or outside clabel. By default, it will be constrained to be INSIDE. For OUTSIDE, specify --clabelinv. clabel must be a surface-based label.  ||
|| --mask-inv || Constrain cluster search to be OUTSIDE mask or clabel.  ||
|| --sum summaryfile || The summary text file (the argument of the --sum flag) will contain a summary of the result of the clustering as well as a summary of the conditions under which the clustering was performed. It will list the clusters (1 to N) along with the maximum value found in the cluster (Max), the vertex at which this maximum value was found (VtxMax), the surface area of the cluster (Size), and the Talaiarach coordinates of the maximum (based on talairach.xfm).  ||
|| --o outputid || File in which to store the surface values after setting the non-cluster vertices to zero. Fmt is the format (currently, only paint format is supported). Note: make sure to put a ./ in front of outputid or else it will attempt to write the output to the subject's surf directory.  ||
|| --ocn ocnid || File in which to store the cluster number of each vertex. This can be useful for determining to which cluster a particular vertex belongs. It can be viewed as with any other surface value file. Fmt is the format (currently, only paint format is supported). Note: make sure to put a ./ in front of outputid or else it will attempt to write the output to the subject's surf directory.  ||
|| --olab outlabelbase || Save output clusters as labels. There will be a label file for each cluster. The name will be outlabelbase-XXXX.label, where XXXX is the 4-digit, zero-paded cluster number. The stat field in the label will be the value of the input statistic at that vertex.  ||
|| --xfm xfmfile || This is a transform file that is used to compute the Talairach coordinates of a vertex for the summary file. The file must be found in subjects_dir/subjectid/transforms. The default is talairach.xfm which is based on the MNI atlas (see --fixmni).  ||
|| --fixmni --nofixmni || Fix (or do not fix) MNI Talairach coordinates based on Matthew Brett's transform. See http://www.mrc-cbu.cam.ac.uk/Imaging/mnispace.html. Default is to fix. The user may elect not to fix if the xfm file is not talairach.xfm (see --xfm).  ||
|| --sd subjects_dir || This allows the user to change the FreeSurfer subjects's directory from the command-line. If unspecified, it will be set to the environment variable SUBJECTS_DIR  ||