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.bitt...@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.bitt...@fz-juelich.de
-----Ursprüngliche Nachricht-----
Von: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@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.bitt...@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.bitt...@fz-juelich.de
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Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
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