... at least when I did that, it worked (make sure all metrics are XML_BASE64_GZIP, too), and I got these results:
http://brainmap.wustl.edu/pub/donna/US/UNC/LEFT-RIGHT.VertexArea.zip login pub password download Omitted is the huge TFCE metric output, but the report, label gii, and significance metric are there. Note that for a two-tailed test (our norm), we use alpha of 0.025, because we usually do both hems. On Apr 17, 2012, at 4:12 PM, Donna Dierker wrote: > 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 _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
