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/
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/
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Douglas N Greve -
Stephen Politzer-Ahles