Hi Donna, I have uploaded the file 0yrVertexArea.rar, which contain all the files and command used for TFCE. Please help to find the potential problem.
Thanks a lot, Gang > And all four of these files exist and are colocated with the .metric: > LEFT-RIGHT.VertexArea.tmap.random.5000x.metric.data1 > LEFT-RIGHT.VertexArea.tmap.random.5000x.metric.data2 > LEFT-RIGHT.VertexArea.tmap.random.5000x.metric.data3 > LEFT-RIGHT.VertexArea.tmap.random.5000x.metric.data4 > If so, then please upload not only the script you are running, but also > the standard output/error you get when you run it. For example, if you do > this: > paired.sh > ... instead do: > paired.sh >& paired.out.txt > ... and upload paired.out.txt > On Apr 16, 2012, at 10:22 PM, gangli wrote: > >* Hi Donna, > *> > * *>* I used 64bit windows version, before conversion the metric file is > about 4Megabyte, but after conversion the metric file become 4Gigabyte. And > the error message of command significance-threshold-free is the same as the > previous one. > *> > * *>* Thanks, > *>* Gang > *> > * *> > * *> > * *>* Hi Gang, > *>* I have seen that error before. You uploaded the metric, but there > should also be associated > LEFT-RIGHT.VertexArea.tmap.random.5000x.metric.data1-4 files. Make sure > those exist and did not get moved/deleted accidentally. > *>* Also consider using a caret_command.exe from an older distribution, > e.g.: > *>* > http://brainmap.wustl.edu/pub/caret/caret_distribution_Windows32.v5.62.zip > *>* login pub > *>* password download > *>* Specifically, I think the caret_command -file-convert steps between > the smoothing and TFCE steps might work better with the older version. I > suspect the error below might be a file conversion glitch resulting from > your particular caret_command.exe, but we won't know if that's true unless > it works with an older one. (Note that the only things caret_command is > being used for in this script is conversion to XML and smoothing.) > *>* I recently ran into conversion problems with certain versions of > caret_command. > *>* If you capture the output of the script to a file, does caret_command > complain during the conversion steps? > *>* Donna > *>* On Apr 16, 2012, at 10:27 AM, gangli wrote: > *>* > Hi Donna, > *>* > > *>* > I have done 5000 iteration of the permutation, but when I am trying > to use the command: significance-threshold-free, I saw some errors. I have > upload the file: LEFT-RIGHT.VertexArea.tmap.random.5000x.metric, could you > please help check the errors? > *>* > > *>* > Apr 16, 2012 11:10:52 AM > edu.wustl.caret.niftilib.NiftiXmlFileEntityResolver resolveEntity > *>* > INFO: Resolving: > http://www.nitrc.org/frs/download.php/1594/gifti.dtd > *>* > Apr 16, 2012 11:10:52 AM > edu.wustl.caret.niftilib.NiftiXmlFileEntityResolver resolveEntity > *>* > INFO: Ignoring null > http://www.nitrc.org/frs/download.php/1594/gifti.dtd > *>* > Apr 16, 2012 11:10:52 AM > edu.wustl.caret.giftijlib.GiftiDataArrayFile readFile > *>* > SEVERE: SAX Exception > *>* > org.xml.sax.SAXException: While reading line 1, column 1:Content is > not allowed in prolog. > *>* > at > edu.wustl.caret.niftilib.NiftiXmlDefaultHandler.fatalError(NiftiXmlDefaultHandler.java:45) > *>* > at > com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:180) > *>* > at > com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:441) > *>* > at > com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:368) > *>* > at > com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1375) > *>* > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:996) > *>* > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:607) > *>* > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:488) > *>* > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:835) > *>* > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:764) > *>* > at > com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:123) > *>* > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1210) > *>* > at > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:568) > *>* > at > edu.wustl.caret.giftijlib.GiftiDataArrayFile.readFile(GiftiDataArrayFile.java:724) > *>* > at > edu.wustl.caret.files.GiftiDataArrayBasedFile.readGiftiXmlFormat(GiftiDataArrayBasedFile.java:976) > *>* > at > edu.wustl.caret.files.AbstractFile.readFilesData(AbstractFile.java:1292) > *>* > at > edu.wustl.caret.files.AbstractFile.readFileOnDisk(AbstractFile.java:1199) > *>* > at > edu.wustl.caret.files.AbstractFile.readFile(AbstractFile.java:972) > *>* > at > edu.wustl.caret.statistics.StatisticOperationSignificanceTFCE.executeOperation(StatisticOperationSignificanceTFCE.java:319) > *>* > at > edu.wustl.caret.statistics.StatisticMain.main(StatisticMain.java:120) > *>* > > *>* > ERROR: edu.wustl.caret.giftijlib.GiftiException: > org.xml.sax.SAXException: While reading line 1, column 1:Content is not > allowed in prolog. > *>* > > *>* > > *>* > Thanks a lot, > *>* > Gang*
_______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
