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 > > > I realized coord anova doesn't do what you need, because it's more like a two > sample t-test than a paired t-test (but you can have more than two groups). > It doesn't take the pairing into account. As far as I know, caret_stats > doesn't do what you need it to do for the coords. > If you can use something like local shape mancova > (http://www.insight-journal.org/browse/publication/694) to generate your stat > maps, then you can feed them to caret_stats' TFCE. But again, we're back to > the randomization problem. I don't think that tool will generate the > randomized stat maps using a strategy like those in Nichols & Holmes' primer > paper. > But you can do a paired diff on the depth maps. Just make sure the composites > have the columns in corresponding sequence. > Sorry to get your hopes up on the coords. > On Apr 5, 2012, at 4:40 PM, Donna Dierker wrote: > > I put three scripts here: > > > > http://brainmap.wustl.edu/pub/donna/US/UNC/ > > login pub > > password download > > > > For the coords, you'll need a different test -- coord anova: > > > > http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation:Statistics#Coordinate_Difference_Analysis_of_Variance > > > > One of those scripts does that. But first, you'll need to x-flip either the > > right or left. I propose x-flipping the left to right, resulting in mostly > > positive values for x. See flip-x.sh. > > > > For your depth, you need to make a composite from your depth files, and the > > gen_distortion.sh script does that for distortion. You'll want to recompute > > your distortion using something like that, because the order of the mean > > fiducial and the individual's fiducial is important. The mean is the first > > argument to the distortion command. Else you end up with mostly negative > > values, as you apparently did, and as I did when I first recomputed my > > term12 version 2 distortion metric. Easy mistake to make, but we want to > > pump up areas -- not shrink them down. > > > > Anyway, that script shows how to generate a composite and compute an > > average. You only need the composite for your depth case, but the latter > > comes in handy. > > > > (The gen_distortion.sh script didn't exist when it first came up the other > > day. I just needed to do it, so now it does.) > > > > Donna > > > > > > On Apr 5, 2012, at 10:17 AM, gangli wrote: > > > >> Hi Donna, > >> > >> I would like to test the paired difference between left and right > >> hemispheres on 3D coordinate position and sulcal depth. Please find the > >> uploaded input files and help me figure out how to do this. > >> > >> Thanks a lot. > >> > >> Gang > >> > >> > >> My versions of caret_command can read them all, and the coords/metric all > >> have roughly 164k nodes -- all good. > >> But I still don't have your command line, or inputs like I'd expect to a > >> paired t-test, if that's what you're doing. > >> For each subject, I have a metric that has a column for 3D variability and > >> a column for areal distortion. I doubt that you want to get a paired > >> difference between these disparate measures. > >> What you need, as input to the paired t-test, is a composite metric/shape > >> with one column per subject. One composite might have left sulcal depth, > >> the other right, for example. "It doesn't get any more paired than the > >> left and right hemispheres of a person's brain." --Tom Nichols > >> But it could be thickness at different timepoints, twins' thickness maps > >> -- anything you can pair. But the two composite input files should have > >> equal numbers of columns, and those columns should be paired (i.e., first > >> col of each file corresponds to one another; second col of each file > >> corresponds to one another; and so on). > >> Hope this helps. > >> On Apr 4, 2012, at 1:02 PM, gangli wrote: > >>> Hi Donna, > >>> > >>> I have uploaded several generated subjects along with metric and shape > >>> files. Can you please help me figure out how to average and compose the > >>> shape and metric files? > >>> > >>> Thanks a lot. > >>> > >>> Gang > >>> > >>> Hi Gang, > >>> Could you provide the full command line and/or output from running the > >>> script? It might not work in Windows, but on Linux or MacOSX command line > >>> you would do: > >>> paired.sh >& paired.log > >>> Then upload paired.log here: > >>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi > >>> Depending on what information that gives me, I may want to see more > >>> information, like your mean midthickness, distortion metric, composite > >>> scalar files, etc. > >>> Also, it would be helpful if when you reply you keep the prior message > >>> history in your reply, so that I don't have to go to the archives to > >>> remind myself of what you have already done. It is easy to get users > >>> confused -- particularly when I am using this stuff heavily myself. > >>> Thanks much, > >>> Donna > >>> > >>> On Apr 4, 2012, at 9:07 AM, gangli wrote: > >>>> I am using caret_distribution_Windows32.v5.65 and the input is *.metric > >>>> file generated in previous discussion. Thanks. > >>>> > >>>> Regards, > >>>> Gang > >>>> _______________________________________________ > >>>> caret-users mailing list > >>>> caret-users at brainvis.wustl.edu > >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >>> _______________________________________________ > >>> caret-users mailing list > >>> caret-users at brainvis.wustl.edu > >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> _______________________________________________ > >> caret-users mailing list > >> caret-users at brainvis.wustl.edu > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > caret-users at brainvis.wustl.edu > > 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
