Your original labels are not on fsaverage. You need to transfer them to fsaverage using mri_label2label. That should fix your first problem. The 2nd should be fixed by having your ctab go from 0 to 58 with 0 being the unknown label doug
On 08/18/2013 02:51 PM, Stephen Politzer-Ahles wrote: > Hello, > > I have a set of custom labels and I want to plot them all at once on > one brain, so I'm trying to use mris_label2annot for that. However, > I'm getting several problems. Here is an example of what I get: > > http://i.imgur.com/Sw1Z9UT.png > > The labels I'm using were originally defined on a decimated source > space (that was created using the MNE toolbox), so it's normal that > most of them show up as lots of dots rather than contiguous areas. > However, I don't know why some of them actually are showing up as > contiguous areas; when I plot the labels one by one, all of them show > up as series of dots rather than contiguous areas, so it seems that > creating the annotation is messing something up. > > I also have a few other problems that you can't see in the image. > Firstly (and most seriously), the locations of the labels that show up > when I plot this annotation do not at all match where the labels > actually are--that is, if I hover my mouse over one of the labels in > this, it doesn't match where the label actually should be if I plot > that label by itself. > > Secondly, there seems to be some indexing issue with my color lookup > table--I have 58 labels per hemisphere, so I created a color table > that starts at label 0 and goes up to 57 (as per the example at > http://ftp.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles > and the automatically-generated annotations such as > lh.aparc2009s.annot). In my color lookup table, label 0 is called > 'amygdala' and label 1 is called 'anteriorcommisure'. But when I > actually run mris_label2annot, the output seems to suggest that the > program is 1-indexed instead of 0-indexed (because it skips the 0th > label, andlooks for the 57th label, see output snippet below): > > Reading ctab /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab > Number of ctab entries 58 > > $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ > ... > cmdline mris_label2annot --ctab > /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab --subject fsaverage --annot > MRATparc --hemi lh --l lh.amygdala.label --l > lh.anteriorcommissure.label --l lh.anteriornucleus.label --l > lh.ba1.label --l lh.ba10.label --l lh.ba11.label --l lh.ba13.label --l > lh.ba17.label --l lh.ba18.label --l lh.ba19.label --l lh.ba2.label --l > lh.ba20.label --l lh.ba21.label --l lh.ba22.label --l lh.ba23.label > --l lh.ba24.label --l lh.ba25.label --l lh.ba27.label --l > lh.ba28.label --l lh.ba29.label --l lh.ba3.label --l lh.ba30.label --l > lh.ba31.label --l lh.ba32.label --l lh.ba33.label --l lh.ba34.label > --l lh.ba35.label --l lh.ba36.label --l lh.ba37.label --l > lh.ba38.label --l lh.ba39.label --l lh.ba4.label --l lh.ba40.label --l > lh.ba41.label --l lh.ba42.label --l lh.ba43.label --l lh.ba44.label > --l lh.ba45.label --l lh.ba46.label --l lh.ba47.label --l lh.ba5.label > --l lh.ba6.label --l lh.ba7.label --l lh.ba8.label --l lh.ba9.label > --l lh.caudatebody.label --l lh.caudatehead.label --l > lh.caudatetail.label --l lh.corpuscallosum.label --l lh.culmen.label > --l lh.declive.label --l lh.hippocampus.label --l > lh.hypothalamus.label --l lh.mammillarybody.label --l > lh.medialdorsalnucleus.label --l lh.optictract.label --l > lh.pulvinar.label --l lh.putamen.label > ... > subject fsaverage > hemi lh > SUBJECTS_DIR /media/LAPTOP_HD/WW3_newanalysis/subjects > ColorTable /media/LAPTOP_HD/WW3_mrat/MRATparc.ctab > AnnotName MRATparc > nlables 58 > LabelThresh 0 0.000000 > Loading /media/LAPTOP_HD/WW3_newanalysis/subjects/fsaverage/surf/lh.orig > 1 3988503 anteriorcommissure > 2 11811863 anteriornucleus > 3 3957823 ba10 > ... > 56 1326221 pulvinar > 57 14423183 putamen > 58 -1 NOT_FOUND > > Does anyone have suggestions about any or all of these issues? > > Thank you, > Steve Politzer-Ahles > > > Stephen Politzer-Ahles > New York University, Abu Dhabi > Psychology Department > http://www.nyu.edu/projects/politzer-ahles/ > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
