Enter caret_command -file-convert at the command line, and maybe redirect the output to a file, because it is quite lengthy. It will tell you how to convert Freesurfer surfaces.
They'll need to be on a standard mesh. And you can't do a paired test across hemispheres, because there is no node correspondence across hemispheres in Freesurfer-registered surfaces (unless your surfaces are on the fs_LR standard mesh, but then they'd probably be in caret/gifti form already). You can compute a mean fiducial surface for your group using caret_command -surface-average and then use caret_command -surface-distortion to compute the distortion between each of your subject's midthickness surface and the mean midthickness surface. Then you can average the distortion maps to get a mean distortion map for input to TFCE. The purpose of this file is to correct for the fact that regions of high variability will have lower surface area in the mean fiducial, on which the surface areas for TFCE are calculated. The distortion metric pumps up areas in these regions. Notice that I never said any of this would be easy. On Mar 30, 2012, at 2:40 PM, gangli wrote: > 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 > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
