Your trouble packing up those files will be rewarded if you execute: caret_command -file-convert -format-convert XML_BASE64_GZIP *topo
On Apr 17, 2012, at 1:57 PM, gangli wrote: > 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
