It does look like the problem is the rh.orig. Do you have read permissions for that file? It may be that the file is corrupt. Can you load just that file in freeview or tksurfer? If not, you can try to regenerate it by running mris_fix_topology (look in the subject/scripts/recon-all.log file for command).
On 6/20/16 8:47 PM, Bittner, Nora wrote:
Hi Bruce,
thanks, I will have a closer look to my annotation / label files I used, maybe something is wrong with them. I am happy to get an answer anyway. I already attached the full commandline and the full terminal ouptput - didn´t you get the attached files? Is there another way to send you the files?
My command line was:
mris_label2annot --h rh --subject 995005 --ctab /data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt --a fronparnetwork --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/rh.cortex.label --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob1_nonlinear.label --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob3_nonlinear.label --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob5_nonlinear.label --nhits nhits.mgh
And the terminal output (the full output is too big to simply copy it here - so I will attach the file again):
reading ctab /data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt Number of ctab entries 5
$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /data/Team_Caspers/Bittner/Skripte_Freesurfer cmdline mris_label2annot --h rh --subject 995005 --ctab /data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt --a fronparnetwork --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/rh.cortex.label --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob1_nonlinear.label --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob3_nonlinear.label --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob5_nonlinear.label --nhits nhits.mgh sysname Linux hostname imecas08 machine x86_64 user cjockwitz
subject 995005 hemi rh SUBJECTS_DIR /data/Team_Caspers/1000Brains-Projects/Freesurfer ColorTable /data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt AnnotName fronparnetwork NHitsFile nhits.mgh nlables 4 LabelThresh 0 0.000000 Loading /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.orig 1 -1 NOT_FOUND 2 255 $SUBJECTS_DIR/995005/label/mask_Blob1_nonlinear.label WARNING: vertex 77969 maps to multiple labels! (overwriting) .... (Warning message for many vertices) ... WARNING: vertex 68151 maps to multiple labels! (overwriting) Mapping unhit to unknown Found 8016 unhit vertices Writing annot to /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/rh.fronparnetwork.annot
Thank you for helping me! Best regards, Nora
Arbeitsgruppe Konnektivität Institut für Neurowissenschaften und Medizin (INM-1) Forschungszentrum Jülich GmbH 52425 Jülich Tel.: 02461-612412 Email: n.bittner@fz-juelich.de
und
Arbeitsgruppe Konnektivität im menschlichen Gehirn C. und O. Vogt Institut für Hirnforschung Heinrich-Heine-Universität Düsseldorf Universitätsklinikum Düsseldorf 40225 Düsseldorf Tel.: 0211-8106109 Email: n.bittner@fz-juelich.de
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Montag, 20. Juni 2016 18:28 An: Freesurfer support list Betreff: Re: [Freesurfer] Error loading a constructed annotation file
Hi Nora
sorry for the long response time. Doug is on vacation and that slows everything down! Can you send the full command line and full terminal output? I think the "1 -1 NOT_FOUND ..." error refers to not being able to find an annotation/parcellation NOT to the orig surface.
cheers Bruce
On Fri, 17 Jun 2016, Bittner, Nora wrote:
Dear Bruce,
thank you for your quick reply. Attached I send you the command line, the color table I used, the terminal output from mris_label2annot and the error message that appears when loading my annotation file into freeview. In the terminal output of mris_label2annot I recognized an error message in line 21. It seems that the rh.orig surface can´t be found, although it actual is in the subject´s folder ( I controlled this twice). I don´t understand this. I will put the first lines here, but the complete terminal output of mris_label2annot is attached.
Terminal Output: "Reading ctab /data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt Number of ctab entries 5
$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /data/Team_Caspers/Bittner/Skripte_Freesurfer cmdline mris_label2annot --h rh --subject 995005 --ctab /data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt --a fronparnetwork --l /data/Team_Caspers/1000Brains- Projects/Freesurfer/995005/label/rh.cortex.label --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob1_nonlinear.label --l /data/Team_Caspers/1000Brains- Projects/Freesurfer/995005/label/mask_Blob3_nonlinear.label --l /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/label/mask_Blob5_nonlinear.label --nhits nhits.mgh sysname Linux hostname imecas08 machine x86_64 user cjockwitz
subject 995005 hemi rh SUBJECTS_DIR /data/Team_Caspers/1000Brains-Projects/Freesurfer ColorTable /data/Team_Caspers/1000Brains-Projects/Freesurfer/rh.fronparnetwork.txt AnnotName fronparnetwork NHitsFile nhits.mgh nlables 4 LabelThresh 0 0.000000 Loading /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.orig 1 -1 NOT_FOUND ..."
Might this be the problem?
Thank you in advance,
Nora
Arbeitsgruppe Konnektivität Institut für Neurowissenschaften und Medizin (INM-1) Forschungszentrum Jülich GmbH 52425 Jülich Tel.: 02461-612412 Email: n.bittner@fz-juelich.de
und
Arbeitsgruppe Konnektivität im menschlichen Gehirn C. und O. Vogt Institut für Hirnforschung Heinrich-Heine-Universität Düsseldorf Universitätsklinikum Düsseldorf 40225 Düsseldorf Tel.: 0211-8106109 Email: n.bittner@fz-juelich.de
-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Donnerstag, 16. Juni 2016 16:54 An: Freesurfer support list Betreff: Re: [Freesurfer] Error loading a constructed annotation file
Hi Nora
you need to send us the complete command line you ran and also the error message and the complete terminal outpu
cheers Bruce On Thu, 16 Jun 2016, Bittner, Nora wrote:
Dear freesurfer experts,
I constructed an annotation file using mris_label2annot. I did this several times and every time it worked very well. I was able to use a ctab to define several colors, load my annotation file into freeview, and look at it.
Now I tried to construct another annotation file in the same manner, but if I try to load it into freeview, freeview just crashes. When I constructed the annotation file I received no error from the terminal output.
I can´t understand the error message the terminal gives in the moment freeview crashes. Since I was always successful in constructing my annotation files, I wonder why this happens now.
I hope you can tell me, what the attached error message means.
Thanking you in advance,
Nora Bittner
Arbeitsgruppe Konnektivität
Institut für Neurowissenschaften und Medizin (INM-1) Forschungszentrum Jülich GmbH 52425 Jülich Tel.: 02461-612412 Email: n.bittner@fz-juelich.deund
Arbeitsgruppe Konnektivität im menschlichen Gehirn
C. und O. Vogt Institut für Hirnforschung Heinrich-Heine-Universität Düsseldorf Universitätsklinikum Düsseldorf 40225 Düsseldorf Tel.: 0211-8106109 Email: n.bittner@fz-juelich.de
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