Thanks for your quick answer.
Yes, I have read permissions for that file. I can also load the rh.orig into freeview without any error message appearing in the terminal. Looks quite nice.
I tried using mris_fix_topology by taking the exact command from the recon-all.log of the particular subject. And that indeed gives me an error message:
My command:
mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 995005 rh > $SUBJECTS_DIR/995005/scripts/mris_fix_topology 2> $SUBJECTS_DIR/995005/scripts/mris_fix_topology
Full terminal output:
INFO: assuming .mgz format
$Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
reading input surface /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
0
number of generations : 10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient : 10.0
normal dot loglikelihood coefficient : 1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search : 1
initial patch selection : 1
select all defect vertices : 0
ordering dependant retessellation: 0
use precomputed edge table : 0
smooth retessellated patch : 2
match retessellated patch : 1
verbose mode : 0
*************************************************************
before topology correction, eno=-30 (nv=140324, nf=280708, ne=421062, g=16)
mrisReadTriangleFile(/data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.orig): surface doesn't match /data/Team_Caspers/1000Brains-Projects/Freesurfer/995005/surf/rh.qsphere.nofix
Invalid argument
mrisReadTriangleFile failed.
Invalid argument
MRISreadOriginalProperties: could not read surface file orig
Invalid argument
mris_fix_topology: could not read original surface orig
Invalid argument
Seems like there is a mismatch between rh.orig and rh.qsphere.nofix. I never modified rh.orig. Do you have any idea, how this can happen?
Thank you very much!
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
Von: freesurfer-bounces@nmr.mgh.harvard.edu
[mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Douglas Greve
Gesendet: Dienstag, 21. Juni 2016 10:22
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] Error loading a constructed annotation file
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.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
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