Hi Donna,
Than you for preparing the software package. Right now all my surfaces are
in FreeSurfer format, so how should I convert the files into Caret format,
since many inputs are required, for example the [-distortion-file
distortion-metric-shape-file-name] ?
Signficance - Threshold Free
-significance-threshold-free
<-statistic-file statistic-file-name>
<-statistic-file-column column-name-or-index>
<-output-statistic-file output-statistic-file-name>
<-random-file randomized-file-name>
[-output-randomized-file output-random-file-name]
<-coordinate-file coordinate-file-name>
<-topology-file topology-file-name>
<-significance-level value>
<-output-label-file label-file-name>
<-output-report-file report-file-name>
[-distortion-file distortion-metric-shape-file-name]
[-distortion-file-column column-name-or-index]
[-number-of-threads value]
[-print-progress-message]
[-E extent]
[-H height]
[-monotonic]
[-threshold-positive value]
[-threshold-negative value]
[-output-file-encoding encoding-type]
[-randomized-output-file-encoding encoding-type]
Set the significance levels for nodes using the threshold-
free cluster enhancement algorithm adapted for surface-
based data.
* Transform the specified column in the statistic
file using the TFCE enhancement function.
* Transform all columns in the randomized file using
the TFCE enhancement function.
* Find the greatest TFCE-enhanced value in each of the
randomized files columns. Rank these values from
largest to smallest, assigning P-Values based upon
their ranks so that the largest value has a P-Value
of 0.0 and the smallest values a P-Value of 1.0
* For each node in the specified column of the
statistic file, compare its value to the ranked
values and assign the node its P-Value.
Set threshold free significance levels.
* Find and rank the largest absolute value in each
column of the randomized file where each column is
a TFCE transformed statistic generated from.
permuted data.
* For each value in the input files TFCE column, find
its ranking in the ranked, random TFCE data and
generate the significance level (p-value).
* Add the P and/or Q values to the output file.
The statistic file column may be specified by either its
name or by its column index with the first column at
index 1.
The output randomized file is optional. Creating the
output randomized file may use so much memory that the
program will fail with an out of memory error.
The thresholds should only be used if "-monotonic"
(the slot monotonic algorithm) is being used.
If the number-of-threads-to-run is greater than one,
the TFCE enhancement of the randomized file is run in
parallel using the specified number of threads.
The distortion file is used to correct for surface
distortion that may occur in the case of surface
averaging. The distortion file column may be specified
with either its name or by its column index with the first
column at index 1.
If "-print-progress-message" is specified, a message
is printed as each randomized file column is searched.
Add the "-monotonic" option to run the old TFCE algorithm which is very
slow
The default value for "-E" (extent) is 1.0
The default value for "-H" (height) is 2.0
The available output file encodings are:
GIFTI
GIFTI-BASE64
GIFTI-GZIP
GIFTI-EXTERNAL
"GIFTI" is a XML file with all data in text format.
Files in this format are the largest and take the
longest time to read of the GIFTI formats.
"GIFTI-BASE64" is an XML file with the binary data
encoded as Base64 text.
"GIFTI-GZIP" is an XML file with the binary data
compressed using the the GZIP algorithm with the
binary data encoded using Base64 text. Files in this
format are smaller than the other GIFTI formats and
usually take the least time to read.
"GIFTI-EXTERNAL" is an XML file with the data stored
in an separate, external, uncompressed file.
The default output file encoding is GIFTI-GZIP
The default output randomized file encoding is GIFTI-EXTERNAL
Regards,
Gang
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